https://launchpad.net/ubuntu/+archive/test-rebuild-20181222/+build/16009151 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-019 4.4.0-141-generic #167-Ubuntu SMP Wed Dec 5 10:40:15 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 28 Jan 10:24:07 ntpdate[1812]: adjust time server 10.211.37.1 offset 0.003455 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-16009151 /home/buildd/filecache-default/ccc8a783f4c9fcf0282a95411cd13cfaeeda0fbe Creating target for build PACKAGEBUILD-16009151 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-16009151 Starting target for build PACKAGEBUILD-16009151 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-16009151 'deb http://ftpmaster.internal/ubuntu bionic main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-updates main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-16009151 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-16009151 Updating target for build PACKAGEBUILD-16009151 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [242 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [88.7 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [88.7 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main i386 Packages [1007 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main Translation-en [516 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/universe i386 Packages [8531 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4941 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/multiverse i386 Packages [144 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-security/main i386 Packages [186 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-security/main Translation-en [92.3 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-security/universe i386 Packages [112 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-security/universe Translation-en [64.4 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-security/multiverse i386 Packages [3500 B] Get:14 http://ftpmaster.internal/ubuntu bionic-security/multiverse Translation-en [1848 B] Get:15 http://ftpmaster.internal/ubuntu bionic-updates/main i386 Packages [426 kB] Get:16 http://ftpmaster.internal/ubuntu bionic-updates/main Translation-en [184 kB] Get:17 http://ftpmaster.internal/ubuntu bionic-updates/restricted i386 Packages [6928 B] Get:18 http://ftpmaster.internal/ubuntu bionic-updates/restricted Translation-en [3076 B] Get:19 http://ftpmaster.internal/ubuntu bionic-updates/universe i386 Packages [706 kB] Get:20 http://ftpmaster.internal/ubuntu bionic-updates/universe Translation-en [177 kB] Get:21 http://ftpmaster.internal/ubuntu bionic-updates/multiverse i386 Packages [6540 B] Get:22 http://ftpmaster.internal/ubuntu bionic-updates/multiverse Translation-en [3356 B] Fetched 17.5 MB in 6s (3137 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files binutils binutils-common binutils-i686-linux-gnu bsdutils cpp cpp-7 dpkg dpkg-dev e2fslibs e2fsprogs fdisk g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base gpg gpg-agent gpgconf gpgv libapparmor1 libapt-pkg5.0 libasan4 libatomic1 libbinutils libblkid1 libcc1-0 libcilkrts5 libcom-err2 libcomerr2 libcryptsetup12 libdpkg-perl libext2fs2 libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgomp1 libitm1 libkmod2 libmount1 libmpx2 libncurses5 libncursesw5 libperl5.26 libpng16-16 libprocps6 libquadmath0 libsmartcols1 libss2 libssl1.1 libstdc++-7-dev libstdc++6 libsystemd0 libtinfo5 libubsan0 libudev1 libuuid1 linux-libc-dev mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.26 pkgbinarymangler procps systemd systemd-sysv tzdata ubuntu-keyring util-linux 76 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 53.7 MB of archives. After this operation, 267 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic-updates/main i386 base-files i386 10.1ubuntu2.3 [60.5 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-updates/main i386 bsdutils i386 1:2.31.1-0.4ubuntu3.3 [62.7 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates/main i386 dpkg i386 1.19.0.5ubuntu2.1 [1163 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libext2fs2 i386 1.44.1-1ubuntu1 [185 kB] Get:5 http://ftpmaster.internal/ubuntu bionic-updates/main i386 e2fsprogs i386 1.44.1-1ubuntu1 [428 kB] Get:6 http://ftpmaster.internal/ubuntu bionic-updates/main i386 ncurses-bin i386 6.1-1ubuntu1.18.04 [165 kB] Get:7 http://ftpmaster.internal/ubuntu bionic-security/main i386 libperl5.26 i386 5.26.1-6ubuntu0.3 [3184 kB] Get:8 http://ftpmaster.internal/ubuntu bionic-security/main i386 perl i386 5.26.1-6ubuntu0.3 [201 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-security/main i386 perl-base i386 5.26.1-6ubuntu0.3 [1495 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-security/main i386 perl-modules-5.26 all 5.26.1-6ubuntu0.3 [2763 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libuuid1 i386 2.31.1-0.4ubuntu3.3 [20.9 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libblkid1 i386 2.31.1-0.4ubuntu3.3 [140 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libfdisk1 i386 2.31.1-0.4ubuntu3.3 [183 kB] Get:14 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libmount1 i386 2.31.1-0.4ubuntu3.3 [149 kB] Get:15 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libncurses5 i386 6.1-1ubuntu1.18.04 [101 kB] Get:16 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libtinfo5 i386 6.1-1ubuntu1.18.04 [80.4 kB] Get:17 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libncursesw5 i386 6.1-1ubuntu1.18.04 [128 kB] Get:18 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libsmartcols1 i386 2.31.1-0.4ubuntu3.3 [92.1 kB] Get:19 http://ftpmaster.internal/ubuntu bionic-updates/main i386 fdisk i386 2.31.1-0.4ubuntu3.3 [116 kB] Get:20 http://ftpmaster.internal/ubuntu bionic-updates/main i386 util-linux i386 2.31.1-0.4ubuntu3.3 [930 kB] Get:21 http://ftpmaster.internal/ubuntu bionic-updates/main i386 ncurses-base all 6.1-1ubuntu1.18.04 [17.8 kB] Get:22 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libquadmath0 i386 8.2.0-1ubuntu2~18.04 [208 kB] Get:23 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libmpx2 i386 8.2.0-1ubuntu2~18.04 [12.9 kB] Get:24 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libitm1 i386 8.2.0-1ubuntu2~18.04 [30.8 kB] Get:25 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libgomp1 i386 8.2.0-1ubuntu2~18.04 [80.8 kB] Get:26 http://ftpmaster.internal/ubuntu bionic-updates/main i386 gcc-8-base i386 8.2.0-1ubuntu2~18.04 [18.3 kB] Get:27 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libgcc1 i386 1:8.2.0-1ubuntu2~18.04 [48.1 kB] Get:28 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libcc1-0 i386 8.2.0-1ubuntu2~18.04 [41.9 kB] Get:29 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libatomic1 i386 8.2.0-1ubuntu2~18.04 [9632 B] Get:30 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libstdc++6 i386 8.2.0-1ubuntu2~18.04 [430 kB] Get:31 http://ftpmaster.internal/ubuntu bionic-security/main i386 libudev1 i386 237-3ubuntu10.11 [57.7 kB] Get:32 http://ftpmaster.internal/ubuntu bionic-security/main i386 libapt-pkg5.0 i386 1.6.6ubuntu0.1 [872 kB] Get:33 http://ftpmaster.internal/ubuntu bionic-security/main i386 libgcrypt20 i386 1.8.1-4ubuntu1.1 [399 kB] Get:34 http://ftpmaster.internal/ubuntu bionic-security/main i386 gpgv i386 2.2.4-1ubuntu1.2 [218 kB] Get:35 http://ftpmaster.internal/ubuntu bionic-updates/main i386 ubuntu-keyring all 2018.09.18.1~18.04.0 [22.4 kB] Get:36 http://ftpmaster.internal/ubuntu bionic-security/main i386 apt i386 1.6.6ubuntu0.1 [1193 kB] Get:37 http://ftpmaster.internal/ubuntu bionic-security/main i386 libapparmor1 i386 2.12-4ubuntu5.1 [32.7 kB] Get:38 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libcryptsetup12 i386 2:2.0.2-1ubuntu1.1 [150 kB] Get:39 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libkmod2 i386 24-1ubuntu3.1 [46.4 kB] Get:40 http://ftpmaster.internal/ubuntu bionic-updates/main i386 mount i386 2.31.1-0.4ubuntu3.3 [112 kB] Get:41 http://ftpmaster.internal/ubuntu bionic-security/main i386 libprocps6 i386 2:3.3.12-3ubuntu1.1 [32.7 kB] Get:42 http://ftpmaster.internal/ubuntu bionic-security/main i386 procps i386 2:3.3.12-3ubuntu1.1 [224 kB] Get:43 http://ftpmaster.internal/ubuntu bionic-security/main i386 systemd i386 237-3ubuntu10.11 [2954 kB] Get:44 http://ftpmaster.internal/ubuntu bionic-security/main i386 libsystemd0 i386 237-3ubuntu10.11 [221 kB] Get:45 http://ftpmaster.internal/ubuntu bionic-security/main i386 systemd-sysv i386 237-3ubuntu10.11 [12.0 kB] Get:46 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libcom-err2 i386 1.44.1-1ubuntu1 [9668 B] Get:47 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libss2 i386 1.44.1-1ubuntu1 [11.6 kB] Get:48 http://ftpmaster.internal/ubuntu bionic-security/main i386 libssl1.1 i386 1.1.0g-2ubuntu4.3 [1124 kB] Get:49 http://ftpmaster.internal/ubuntu bionic-security/main i386 openssl i386 1.1.0g-2ubuntu4.3 [541 kB] Get:50 http://ftpmaster.internal/ubuntu bionic-security/main i386 tzdata all 2018i-0ubuntu0.18.04 [189 kB] Get:51 http://ftpmaster.internal/ubuntu bionic-security/main i386 libpng16-16 i386 1.6.34-1ubuntu0.18.04.1 [184 kB] Get:52 http://ftpmaster.internal/ubuntu bionic-updates/main i386 binutils-i686-linux-gnu i386 2.30-21ubuntu1~18.04 [2028 kB] Get:53 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libbinutils i386 2.30-21ubuntu1~18.04 [545 kB] Get:54 http://ftpmaster.internal/ubuntu bionic-updates/main i386 binutils i386 2.30-21ubuntu1~18.04 [3392 B] Get:55 http://ftpmaster.internal/ubuntu bionic-updates/main i386 binutils-common i386 2.30-21ubuntu1~18.04 [193 kB] Get:56 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libubsan0 i386 7.3.0-27ubuntu1~18.04 [141 kB] Get:57 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libasan4 i386 7.3.0-27ubuntu1~18.04 [361 kB] Get:58 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libcilkrts5 i386 7.3.0-27ubuntu1~18.04 [47.4 kB] Get:59 http://ftpmaster.internal/ubuntu bionic-updates/main i386 g++-7 i386 7.3.0-27ubuntu1~18.04 [7817 kB] Get:60 http://ftpmaster.internal/ubuntu bionic-updates/main i386 gcc-7 i386 7.3.0-27ubuntu1~18.04 [7698 kB] Get:61 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libstdc++-7-dev i386 7.3.0-27ubuntu1~18.04 [1505 kB] Get:62 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libgcc-7-dev i386 7.3.0-27ubuntu1~18.04 [2399 kB] Get:63 http://ftpmaster.internal/ubuntu bionic-updates/main i386 cpp-7 i386 7.3.0-27ubuntu1~18.04 [6966 kB] Get:64 http://ftpmaster.internal/ubuntu bionic-updates/main i386 gcc-7-base i386 7.3.0-27ubuntu1~18.04 [18.9 kB] Get:65 http://ftpmaster.internal/ubuntu bionic-updates/main i386 cpp i386 4:7.3.0-3ubuntu2.1 [27.6 kB] Get:66 http://ftpmaster.internal/ubuntu bionic-updates/main i386 dpkg-dev all 1.19.0.5ubuntu2.1 [608 kB] Get:67 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libdpkg-perl all 1.19.0.5ubuntu2.1 [211 kB] Get:68 http://ftpmaster.internal/ubuntu bionic-updates/main i386 e2fslibs i386 1.44.1-1ubuntu1 [2712 B] Get:69 http://ftpmaster.internal/ubuntu bionic-updates/main i386 gcc i386 4:7.3.0-3ubuntu2.1 [5248 B] Get:70 http://ftpmaster.internal/ubuntu bionic-updates/main i386 g++ i386 4:7.3.0-3ubuntu2.1 [1580 B] Get:71 http://ftpmaster.internal/ubuntu bionic-security/main i386 gpg i386 2.2.4-1ubuntu1.2 [507 kB] Get:72 http://ftpmaster.internal/ubuntu bionic-security/main i386 gpgconf i386 2.2.4-1ubuntu1.2 [131 kB] Get:73 http://ftpmaster.internal/ubuntu bionic-security/main i386 gpg-agent i386 2.2.4-1ubuntu1.2 [246 kB] Get:74 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libcomerr2 i386 1.44.1-1ubuntu1 [2708 B] Get:75 http://ftpmaster.internal/ubuntu bionic-security/main i386 linux-libc-dev i386 4.15.0-43.46 [1010 kB] Get:76 http://ftpmaster.internal/ubuntu bionic-security/main i386 pkgbinarymangler all 138.18.04.0 [52.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 53.7 MB in 1s (44.7 MB/s) (Reading database ... 12632 files and directories currently installed.) 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Unpacking pkgbinarymangler (138.18.04.0) over (138) ... Setting up libquadmath0:i386 (8.2.0-1ubuntu2~18.04) ... Setting up libgomp1:i386 (8.2.0-1ubuntu2~18.04) ... Setting up libatomic1:i386 (8.2.0-1ubuntu2~18.04) ... Setting up libcc1-0:i386 (8.2.0-1ubuntu2~18.04) ... Setting up pkgbinarymangler (138.18.04.0) ... Setting up e2fslibs:i386 (1.44.1-1ubuntu1) ... Setting up libpng16-16:i386 (1.6.34-1ubuntu0.18.04.1) ... Setting up tzdata (2018i-0ubuntu0.18.04) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jan 28 10:24:45 UTC 2019. Universal Time is now: Mon Jan 28 10:24:45 UTC 2019. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (237-3ubuntu10.11) ... Setting up gpgconf (2.2.4-1ubuntu1.2) ... Setting up linux-libc-dev:i386 (4.15.0-43.46) ... Setting up gpg-agent (2.2.4-1ubuntu1.2) ... Setting up perl-modules-5.26 (5.26.1-6ubuntu0.3) ... Setting up gcc-7-base:i386 (7.3.0-27ubuntu1~18.04) ... Setting up binutils-common:i386 (2.30-21ubuntu1~18.04) ... Setting up libmpx2:i386 (8.2.0-1ubuntu2~18.04) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up libperl5.26:i386 (5.26.1-6ubuntu0.3) ... Setting up libssl1.1:i386 (1.1.0g-2ubuntu4.3) ... Setting up openssl (1.1.0g-2ubuntu4.3) ... Setting up libcomerr2:i386 (1.44.1-1ubuntu1) ... Setting up libitm1:i386 (8.2.0-1ubuntu2~18.04) ... Setting up gpg (2.2.4-1ubuntu1.2) ... Setting up libasan4:i386 (7.3.0-27ubuntu1~18.04) ... Setting up libbinutils:i386 (2.30-21ubuntu1~18.04) ... Setting up libcilkrts5:i386 (7.3.0-27ubuntu1~18.04) ... Setting up libubsan0:i386 (7.3.0-27ubuntu1~18.04) ... Setting up libgcc-7-dev:i386 (7.3.0-27ubuntu1~18.04) ... Setting up cpp-7 (7.3.0-27ubuntu1~18.04) ... Setting up libstdc++-7-dev:i386 (7.3.0-27ubuntu1~18.04) ... Setting up perl (5.26.1-6ubuntu0.3) ... Setting up binutils-i686-linux-gnu (2.30-21ubuntu1~18.04) ... Setting up binutils (2.30-21ubuntu1~18.04) ... Setting up cpp (4:7.3.0-3ubuntu2.1) ... Setting up gcc-7 (7.3.0-27ubuntu1~18.04) ... Setting up g++-7 (7.3.0-27ubuntu1~18.04) ... Setting up libdpkg-perl (1.19.0.5ubuntu2.1) ... Setting up gcc (4:7.3.0-3ubuntu2.1) ... Setting up dpkg-dev (1.19.0.5ubuntu2.1) ... Setting up g++ (4:7.3.0-3ubuntu2.1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-16009151 i386 bionic -c chroot:build-PACKAGEBUILD-16009151 --arch=i386 --dist=bionic --nolog bcftools_1.7-2.dsc Initiating build PACKAGEBUILD-16009151 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-141-generic #167-Ubuntu SMP Wed Dec 5 10:40:15 UTC 2018 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-019.buildd +==============================================================================+ | bcftools 1.7-2 (i386) 28 Jan 2019 10:24 | +==============================================================================+ Package: bcftools Version: 1.7-2 Source Version: 1.7-2 Distribution: bionic Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/bcftools-HklS21/bcftools-1.7' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-HklS21' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-16009151/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bcftools_1.7-2.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-7CEbZh/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-7CEbZh/apt_archive ./ InRelease Get:2 copy:/<>/resolver-7CEbZh/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-7CEbZh/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-7CEbZh/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-7CEbZh/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (97.0 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-7CEbZh/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12639 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl Filtered Build-Depends: debhelper (>= 10), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<>/resolver-yBCEl0/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. Ign:1 copy:/<>/resolver-yBCEl0/apt_archive ./ InRelease Get:2 copy:/<>/resolver-yBCEl0/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-yBCEl0/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-yBCEl0/apt_archive ./ Sources [269 B] Get:5 copy:/<>/resolver-yBCEl0/apt_archive ./ Packages [575 B] Fetched 2963 B in 0s (191 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install bcftools build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu60 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libtimedate-perl libtool libwind0-heimdal libxml2 m4 man-db po-debconf tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu60 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libtimedate-perl libtool libwind0-heimdal libxml2 m4 man-db po-debconf sbuild-build-depends-bcftools-dummy tabix zlib1g-dev 0 upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 22.4 MB of archives. After this operation, 84.6 MB of additional disk space will be used. Get:1 copy:/<>/resolver-yBCEl0/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [904 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main i386 libbsd0 i386 0.8.7-1 [44.7 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main i386 bsdmainutils i386 11.1.2ubuntu1 [184 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main i386 groff-base i386 1.22.3-10 [1169 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main i386 libpipeline1 i386 1.5.0-1 [27.2 kB] Get:6 http://ftpmaster.internal/ubuntu bionic-updates/main i386 man-db i386 2.8.3-2ubuntu0.1 [1029 kB] Get:7 http://ftpmaster.internal/ubuntu bionic-security/main i386 libmagic-mgc i386 1:5.32-2ubuntu0.1 [184 kB] Get:8 http://ftpmaster.internal/ubuntu bionic-security/main i386 libmagic1 i386 1:5.32-2ubuntu0.1 [75.1 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-security/main i386 file i386 1:5.32-2ubuntu0.1 [22.0 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libglib2.0-0 i386 2.56.3-0ubuntu0.18.04.1 [1234 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main i386 libicu60 i386 60.2-3ubuntu3 [8193 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-security/main i386 libxml2 i386 2.9.4+dfsg1-6.1ubuntu1.2 [698 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-security/main i386 gettext-base i386 0.19.8.1-6ubuntu0.1 [51.5 kB] Get:14 http://ftpmaster.internal/ubuntu bionic-security/main i386 libkrb5support0 i386 1.16-2ubuntu0.1 [32.5 kB] Get:15 http://ftpmaster.internal/ubuntu bionic-security/main i386 libk5crypto3 i386 1.16-2ubuntu0.1 [89.6 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main i386 libkeyutils1 i386 1.5.9-9.2ubuntu2 [8968 B] Get:17 http://ftpmaster.internal/ubuntu bionic-security/main i386 libkrb5-3 i386 1.16-2ubuntu0.1 [303 kB] Get:18 http://ftpmaster.internal/ubuntu bionic-security/main i386 libgssapi-krb5-2 i386 1.16-2ubuntu0.1 [132 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main i386 libpsl5 i386 0.19.1-5build1 [42.5 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main i386 libsigsegv2 i386 2.12-1 [15.0 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main i386 m4 i386 1.4.18-1 [196 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main i386 autoconf all 2.69-11 [322 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main i386 autotools-dev all 20180224.1 [39.6 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main i386 automake all 1:1.15.1-3ubuntu2 [509 kB] Get:25 http://ftpmaster.internal/ubuntu bionic-security/main i386 autopoint all 0.19.8.1-6ubuntu0.1 [412 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main i386 libtool all 2.4.6-2 [194 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main i386 dh-autoreconf all 17 [15.8 kB] Get:28 http://ftpmaster.internal/ubuntu bionic-security/main i386 libarchive-zip-perl all 1.60-1ubuntu0.1 [84.6 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main i386 libfile-stripnondeterminism-perl all 0.040-1.1~build1 [13.8 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main i386 libtimedate-perl all 2.3000-2 [37.5 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main i386 dh-strip-nondeterminism all 0.040-1.1~build1 [5208 B] Get:32 http://ftpmaster.internal/ubuntu bionic/main i386 libcroco3 i386 0.6.12-2 [87.7 kB] Get:33 http://ftpmaster.internal/ubuntu bionic-security/main i386 gettext i386 0.19.8.1-6ubuntu0.1 [902 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main i386 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main i386 po-debconf all 1.0.20 [232 kB] Get:36 http://ftpmaster.internal/ubuntu bionic-updates/main i386 debhelper all 11.1.6ubuntu2 [902 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main i386 libroken18-heimdal i386 7.5.0+dfsg-1 [44.8 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main i386 libasn1-8-heimdal i386 7.5.0+dfsg-1 [183 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main i386 libbz2-dev i386 1.0.6-8.1 [28.6 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main i386 libheimbase1-heimdal i386 7.5.0+dfsg-1 [32.1 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main i386 libhcrypto4-heimdal i386 7.5.0+dfsg-1 [92.6 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main i386 libwind0-heimdal i386 7.5.0+dfsg-1 [48.3 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main i386 libhx509-5-heimdal i386 7.5.0+dfsg-1 [118 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main i386 libkrb5-26-heimdal i386 7.5.0+dfsg-1 [232 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main i386 libheimntlm0-heimdal i386 7.5.0+dfsg-1 [16.4 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main i386 libgssapi3-heimdal i386 7.5.0+dfsg-1 [106 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main i386 libsasl2-modules-db i386 2.1.27~101-g0780600+dfsg-3ubuntu2 [15.6 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main i386 libsasl2-2 i386 2.1.27~101-g0780600+dfsg-3ubuntu2 [52.8 kB] Get:49 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libldap-common all 2.4.45+dfsg-1ubuntu1.1 [16.6 kB] Get:50 http://ftpmaster.internal/ubuntu bionic-updates/main i386 libldap-2.4-2 i386 2.4.45+dfsg-1ubuntu1.1 [167 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main i386 libnghttp2-14 i386 1.30.0-1ubuntu1 [83.0 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-1 [58.1 kB] Get:53 http://ftpmaster.internal/ubuntu bionic-security/main i386 libcurl3-gnutls i386 7.58.0-2ubuntu3.5 [236 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/universe i386 libgslcblas0 i386 2.4+dfsg-6 [80.5 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/universe i386 libgsl23 i386 2.4+dfsg-6 [802 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/universe i386 libgsl-dev i386 2.4+dfsg-6 [1042 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/universe i386 libhts2 i386 1.7-2 [322 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main i386 liblzma-dev i386 5.2.2-1.3 [154 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/universe i386 libhts-dev i386 1.7-2 [406 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main i386 libio-pty-perl i386 1:1.08-1.1build4 [30.8 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/universe i386 tabix i386 1.7-2 [352 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main i386 zlib1g-dev i386 1:1.2.11.dfsg-0ubuntu2 [178 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 22.4 MB in 1s (24.9 MB/s) Selecting previously unselected package libbsd0:i386. (Reading database ... 12639 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.8.7-1_i386.deb ... Unpacking libbsd0:i386 (0.8.7-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu1_i386.deb ... Unpacking bsdmainutils (11.1.2ubuntu1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.3-10_i386.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.0-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.3-2ubuntu0.1_i386.deb ... Unpacking man-db (2.8.3-2ubuntu0.1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.32-2ubuntu0.1_i386.deb ... Unpacking libmagic-mgc (1:5.32-2ubuntu0.1) ... 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Unpacking sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Setting up libicu60:i386 (60.2-3ubuntu3) ... Setting up libbz2-dev:i386 (1.0.6-8.1) ... Setting up libarchive-zip-perl (1.60-1ubuntu0.1) ... Setting up libnghttp2-14:i386 (1.30.0-1ubuntu1) ... Setting up libio-pty-perl (1:1.08-1.1build4) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:i386 (2.12-1) ... Setting up libldap-common (2.4.45+dfsg-1ubuntu1.1) ... Setting up libpsl5:i386 (0.19.1-5build1) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:i386 (2.56.3-0ubuntu0.18.04.1) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:i386 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up libsasl2-2:i386 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up gettext-base (0.19.8.1-6ubuntu0.1) ... Setting up libpipeline1:i386 (1.5.0-1) ... Setting up libroken18-heimdal:i386 (7.5.0+dfsg-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:i386 (0.8.7-1) ... Setting up libkrb5support0:i386 (1.16-2ubuntu0.1) ... Setting up libxml2:i386 (2.9.4+dfsg1-6.1ubuntu1.2) ... Setting up libmagic-mgc (1:5.32-2ubuntu0.1) ... Setting up libmagic1:i386 (1:5.32-2ubuntu0.1) ... Setting up libcroco3:i386 (0.6.12-2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up autotools-dev (20180224.1) ... Setting up libheimbase1-heimdal:i386 (7.5.0+dfsg-1) ... Setting up liblzma-dev:i386 (5.2.2-1.3) ... Setting up libkeyutils1:i386 (1.5.9-9.2ubuntu2) ... Setting up bsdmainutils (11.1.2ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgslcblas0:i386 (2.4+dfsg-6) ... Setting up autopoint (0.19.8.1-6ubuntu0.1) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.040-1.1~build1) ... Setting up libk5crypto3:i386 (1.16-2ubuntu0.1) ... Setting up libwind0-heimdal:i386 (7.5.0+dfsg-1) ... Setting up libgsl23:i386 (2.4+dfsg-6) ... Setting up gettext (0.19.8.1-6ubuntu0.1) ... Setting up libgsl-dev (2.4+dfsg-6) ... Setting up libasn1-8-heimdal:i386 (7.5.0+dfsg-1) ... Setting up libhcrypto4-heimdal:i386 (7.5.0+dfsg-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-2ubuntu0.1) ... Setting up libhx509-5-heimdal:i386 (7.5.0+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-3ubuntu2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.3-2ubuntu0.1) ... Not building database; man-db/auto-update is not 'true'. Setting up libkrb5-3:i386 (1.16-2ubuntu0.1) ... Setting up libkrb5-26-heimdal:i386 (7.5.0+dfsg-1) ... Setting up libheimntlm0-heimdal:i386 (7.5.0+dfsg-1) ... Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up libgssapi-krb5-2:i386 (1.16-2ubuntu0.1) ... Setting up libgssapi3-heimdal:i386 (7.5.0+dfsg-1) ... Setting up libldap-2.4-2:i386 (2.4.45+dfsg-1ubuntu1.1) ... Setting up libcurl3-gnutls:i386 (7.58.0-2ubuntu3.5) ... Setting up tabix (1.7-2) ... Setting up libhts2:i386 (1.7-2) ... Setting up libhts-dev:i386 (1.7-2) ... Setting up dh-autoreconf (17) ... Setting up dh-strip-nondeterminism (0.040-1.1~build1) ... Setting up debhelper (11.1.6ubuntu2) ... Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-141-generic amd64 (i686) Toolchain package versions: binutils_2.30-21ubuntu1~18.04 dpkg-dev_1.19.0.5ubuntu2.1 g++-7_7.3.0-27ubuntu1~18.04 gcc-7_7.3.0-27ubuntu1~18.04 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-27ubuntu1~18.04 libstdc++6_8.2.0-1ubuntu2~18.04 linux-libc-dev_4.15.0-43.46 Package versions: adduser_3.116ubuntu1 advancecomp_2.1-1 apt_1.6.6ubuntu0.1 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6ubuntu0.1 autotools-dev_20180224.1 base-files_10.1ubuntu2.3 base-passwd_3.5.44 bash_4.4.18-2ubuntu1 binutils_2.30-21ubuntu1~18.04 binutils-common_2.30-21ubuntu1~18.04 binutils-i686-linux-gnu_2.30-21ubuntu1~18.04 bsdmainutils_11.1.2ubuntu1 bsdutils_1:2.31.1-0.4ubuntu3.3 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20180409 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu2.1 cpp-7_7.3.0-27ubuntu1~18.04 dash_0.5.8-2.10 debconf_1.5.66 debhelper_11.1.6ubuntu2 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.040-1.1~build1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu2.1 dpkg-dev_1.19.0.5ubuntu2.1 e2fslibs_1.44.1-1ubuntu1 e2fsprogs_1.44.1-1ubuntu1 fakeroot_1.22-2ubuntu1 fdisk_2.31.1-0.4ubuntu3.3 file_1:5.32-2ubuntu0.1 findutils_4.6.0+git+20170828-2 g++_4:7.3.0-3ubuntu2.1 g++-7_7.3.0-27ubuntu1~18.04 gcc_4:7.3.0-3ubuntu2.1 gcc-7_7.3.0-27ubuntu1~18.04 gcc-7-base_7.3.0-27ubuntu1~18.04 gcc-8-base_8.2.0-1ubuntu2~18.04 gettext_0.19.8.1-6ubuntu0.1 gettext-base_0.19.8.1-6ubuntu0.1 gpg_2.2.4-1ubuntu1.2 gpg-agent_2.2.4-1ubuntu1.2 gpgconf_2.2.4-1ubuntu1.2 gpgv_2.2.4-1ubuntu1.2 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hostname_3.20 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu5.1 libapt-pkg5.0_1.6.6ubuntu0.1 libarchive-zip-perl_1.60-1ubuntu0.1 libargon2-0_0~20161029-1.1 libasan4_7.3.0-27ubuntu1~18.04 libasn1-8-heimdal_7.5.0+dfsg-1 libassuan0_2.5.1-2 libatomic1_8.2.0-1ubuntu2~18.04 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.2-1ubuntu1 libaudit1_1:2.8.2-1ubuntu1 libbinutils_2.30-21ubuntu1~18.04 libblkid1_2.31.1-0.4ubuntu3.3 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.27-3ubuntu1 libc-dev-bin_2.27-3ubuntu1 libc6_2.27-3ubuntu1 libc6-dev_2.27-3ubuntu1 libcap-ng0_0.7.7-3.1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-1ubuntu2~18.04 libcilkrts5_7.3.0-27ubuntu1~18.04 libcom-err2_1.44.1-1ubuntu1 libcomerr2_1.44.1-1ubuntu1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu1.1 libcurl3-gnutls_7.58.0-2ubuntu3.5 libdb5.3_5.3.28-13.1ubuntu1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu2.1 libext2fs2_1.44.1-1ubuntu1 libfakeroot_1.22-2ubuntu1 libfdisk1_2.31.1-0.4ubuntu3.3 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1.1~build1 libgcc-7-dev_7.3.0-27ubuntu1~18.04 libgcc1_1:8.2.0-1ubuntu2~18.04 libgcrypt20_1.8.1-4ubuntu1.1 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libglib2.0-0_2.56.3-0ubuntu0.18.04.1 libgmp10_2:6.1.2+dfsg-2 libgnutls30_3.5.18-1ubuntu1 libgomp1_8.2.0-1ubuntu2~18.04 libgpg-error0_1.27-6 libgsl-dev_2.4+dfsg-6 libgsl23_2.4+dfsg-6 libgslcblas0_2.4+dfsg-6 libgssapi-krb5-2_1.16-2ubuntu0.1 libgssapi3-heimdal_7.5.0+dfsg-1 libhcrypto4-heimdal_7.5.0+dfsg-1 libheimbase1-heimdal_7.5.0+dfsg-1 libheimntlm0-heimdal_7.5.0+dfsg-1 libhogweed4_3.4-1 libhts-dev_1.7-2 libhts2_1.7-2 libhx509-5-heimdal_7.5.0+dfsg-1 libicu60_60.2-3ubuntu3 libidn11_1.33-2.1ubuntu1 libidn2-0_2.0.4-1.1build2 libio-pty-perl_1:1.08-1.1build4 libip4tc0_1.6.1-2ubuntu2 libisl19_0.19-1 libitm1_8.2.0-1ubuntu2~18.04 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2ubuntu0.1 libkeyutils1_1.5.9-9.2ubuntu2 libkmod2_24-1ubuntu3.1 libkrb5-26-heimdal_7.5.0+dfsg-1 libkrb5-3_1.16-2ubuntu0.1 libkrb5support0_1.16-2ubuntu0.1 libldap-2.4-2_2.4.45+dfsg-1ubuntu1.1 libldap-common_2.4.45+dfsg-1ubuntu1.1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblz4-1_0.0~r131-2ubuntu3 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-2ubuntu0.1 libmagic1_1:5.32-2ubuntu0.1 libmount1_2.31.1-0.4ubuntu3.3 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libmpx2_8.2.0-1ubuntu2~18.04 libncurses5_6.1-1ubuntu1.18.04 libncursesw5_6.1-1ubuntu1.18.04 libnettle6_3.4-1 libnghttp2-14_1.30.0-1ubuntu1 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-9 libperl5.26_5.26.1-6ubuntu0.3 libpipeline1_1.5.0-1 libpng16-16_1.6.34-1ubuntu0.18.04.1 libprocps6_2:3.3.12-3ubuntu1.1 libpsl5_0.19.1-5build1 libquadmath0_8.2.0-1ubuntu2~18.04 libreadline7_7.0-3 libroken18-heimdal_7.5.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.1-2.1ubuntu4 libselinux1_2.7-2build2 libsemanage-common_2.7-2build2 libsemanage1_2.7-2build2 libsepol1_2.7-1 libsigsegv2_2.12-1 libslang2_2.3.1a-3ubuntu1 libsmartcols1_2.31.1-0.4ubuntu3.3 libsqlite3-0_3.22.0-1 libss2_1.44.1-1ubuntu1 libssl1.1_1.1.0g-2ubuntu4.3 libstdc++-7-dev_7.3.0-27ubuntu1~18.04 libstdc++6_8.2.0-1ubuntu2~18.04 libsystemd0_237-3ubuntu10.11 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1-1ubuntu1.18.04 libtool_2.4.6-2 libubsan0_7.3.0-27ubuntu1~18.04 libudev1_237-3ubuntu10.11 libunistring2_0.9.9-0ubuntu1 libusb-0.1-4_2:0.1.12-31 libuuid1_2.31.1-0.4ubuntu3.3 libwind0-heimdal_7.5.0+dfsg-1 libxml2_2.9.4+dfsg1-6.1ubuntu1.2 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.15.0-43.46 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1ubuntu1 man-db_2.8.3-2ubuntu0.1 mawk_1.3.3-17ubuntu3 mount_2.31.1-0.4ubuntu3.3 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1-1ubuntu1.18.04 ncurses-bin_6.1-1ubuntu1.18.04 openssl_1.1.0g-2ubuntu4.3 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.1-6ubuntu0.3 perl-base_5.26.1-6ubuntu0.3 perl-modules-5.26_5.26.1-6ubuntu0.3 pinentry-curses_1.1.0-1 pkgbinarymangler_138.18.04.0 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-3ubuntu1.1 readline-common_7.0-3 sbuild-build-depends-bcftools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_237-3ubuntu10.11 systemd-sysv_237-3ubuntu10.11 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tabix_1.7-2 tar_1.29b-2 tzdata_2018i-0ubuntu0.18.04 ubuntu-keyring_2018.09.18.1~18.04.0 util-linux_2.31.1-0.4ubuntu3.3 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Feb 20 15:51:47 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcftools_1.7-2.dsc dpkg-source: info: extracting bcftools in bcftools-1.7 dpkg-source: info: unpacking bcftools_1.7.orig.tar.gz dpkg-source: info: unpacking bcftools_1.7-2.debian.tar.xz dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying skip_new_test_failing_on_32bit.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-16009151 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-16009151 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-16009151 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.7-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build bcftools-1.7 dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean rm -f config.mk && touch config.mk dh clean dh_auto_clean make -j4 -O distclean make[1]: Entering directory '/<>' rm -f test/*.o test/*~ test/test-rbuf test/test-regidx make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' rm -f gmon.out *.o *~ bcftools version.h plugins/*.so plugins/*.P rm -rf *.dSYM plugins/*.dSYM test/*.dSYM make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/<>' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:81: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:81: the top level configure.ac:81: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:81: the top level configure.ac:81: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:81: the top level configure.ac:81: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:81: 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/i386-linux-gnu/bcftools ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/i386-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -ldl checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/<>' dh_auto_build -a make -j4 -O make[1]: Entering directory '/<>' echo '#define BCFTOOLS_VERSION "1.7"' > version.h make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/i386-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/split.so version.c plugins/split.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -ldl -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -rdynamic -pthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o ccall.o em.o prob1.o kmin.o -lhts -lm -lz -ldl -ldl make[1]: Leaving directory '/<>' make[1]: Entering directory '/<>' gcc -fPIC -shared -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl make[1]: Leaving directory '/<>' dh_auto_test -a make -j4 -O test VERBOSE=1 make[1]: 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 --plugins --exec bgzip= --exec tabix= test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/W7LlGhaRlN/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/W7LlGhaRlN/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/W7LlGhaRlN/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/W7LlGhaRlN/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/W7LlGhaRlN/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/W7LlGhaRlN/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/W7LlGhaRlN/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/W7LlGhaRlN/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/W7LlGhaRlN/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/W7LlGhaRlN/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/W7LlGhaRlN/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/W7LlGhaRlN/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/W7LlGhaRlN/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/W7LlGhaRlN/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/W7LlGhaRlN/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/W7LlGhaRlN/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/W7LlGhaRlN/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/W7LlGhaRlN/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/W7LlGhaRlN/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/W7LlGhaRlN/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/W7LlGhaRlN/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/W7LlGhaRlN/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/W7LlGhaRlN/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/W7LlGhaRlN/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/W7LlGhaRlN/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/W7LlGhaRlN/empty.bcf .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/W7LlGhaRlN/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/check.1.chk /tmp/W7LlGhaRlN/check.2.chk /tmp/W7LlGhaRlN/check.3.chk /tmp/W7LlGhaRlN/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/W7LlGhaRlN/stats.a.vcf.gz /tmp/W7LlGhaRlN/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/W7LlGhaRlN/stats.a.vcf.gz /tmp/W7LlGhaRlN/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/W7LlGhaRlN/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/W7LlGhaRlN/isec.a.vcf.gz /tmp/W7LlGhaRlN/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/W7LlGhaRlN/isec.a.vcf.gz /tmp/W7LlGhaRlN/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/W7LlGhaRlN/isec.a.vcf.gz /tmp/W7LlGhaRlN/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/W7LlGhaRlN/isec.a.vcf.gz /tmp/W7LlGhaRlN/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/W7LlGhaRlN/isec.a.vcf.gz /tmp/W7LlGhaRlN/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/W7LlGhaRlN/isec.a.vcf.gz /tmp/W7LlGhaRlN/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/W7LlGhaRlN/isec.a.vcf.gz /tmp/W7LlGhaRlN/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/W7LlGhaRlN/isec.a.vcf.gz /tmp/W7LlGhaRlN/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/W7LlGhaRlN/isec.a.vcf.gz /tmp/W7LlGhaRlN/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/W7LlGhaRlN/isec.a.vcf.gz /tmp/W7LlGhaRlN/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/W7LlGhaRlN/isec.tab.gz /tmp/W7LlGhaRlN/isec.a.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/W7LlGhaRlN/isec.tab.gz /tmp/W7LlGhaRlN/isec.a.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/W7LlGhaRlN/merge.a.vcf.gz /tmp/W7LlGhaRlN/merge.b.vcf.gz /tmp/W7LlGhaRlN/merge.c.vcf.gz The outputs differ: /<>/test/merge.abc.out /<>/test/merge.abc.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/W7LlGhaRlN/merge.a.vcf.gz /tmp/W7LlGhaRlN/merge.b.vcf.gz /tmp/W7LlGhaRlN/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.abc.out /<>/test/merge.abc.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/W7LlGhaRlN/merge.a.vcf.gz /tmp/W7LlGhaRlN/merge.b.vcf.gz /tmp/W7LlGhaRlN/merge.c.vcf.gz The outputs differ: /<>/test/merge.abc.2.out /<>/test/merge.abc.2.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -Fx /tmp/W7LlGhaRlN/merge.a.vcf.gz /tmp/W7LlGhaRlN/merge.b.vcf.gz /tmp/W7LlGhaRlN/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.abc.2.out /<>/test/merge.abc.2.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/W7LlGhaRlN/merge.a.vcf.gz /tmp/W7LlGhaRlN/merge.b.vcf.gz /tmp/W7LlGhaRlN/merge.c.vcf.gz The outputs differ: /<>/test/merge.abc.3.out /<>/test/merge.abc.3.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -0 /tmp/W7LlGhaRlN/merge.a.vcf.gz /tmp/W7LlGhaRlN/merge.b.vcf.gz /tmp/W7LlGhaRlN/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.abc.3.out /<>/test/merge.abc.3.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/W7LlGhaRlN/merge.2.a.vcf.gz /tmp/W7LlGhaRlN/merge.2.b.vcf.gz The outputs differ: /<>/test/merge.2.none.out /<>/test/merge.2.none.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m none /tmp/W7LlGhaRlN/merge.2.a.vcf.gz /tmp/W7LlGhaRlN/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.2.none.out /<>/test/merge.2.none.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/W7LlGhaRlN/merge.2.a.vcf.gz /tmp/W7LlGhaRlN/merge.2.b.vcf.gz The outputs differ: /<>/test/merge.2.both.out /<>/test/merge.2.both.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m both /tmp/W7LlGhaRlN/merge.2.a.vcf.gz /tmp/W7LlGhaRlN/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.2.both.out /<>/test/merge.2.both.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/W7LlGhaRlN/merge.2.a.vcf.gz /tmp/W7LlGhaRlN/merge.2.b.vcf.gz The outputs differ: /<>/test/merge.2.all.out /<>/test/merge.2.all.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m all /tmp/W7LlGhaRlN/merge.2.a.vcf.gz /tmp/W7LlGhaRlN/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.2.all.out /<>/test/merge.2.all.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/W7LlGhaRlN/merge.3.a.vcf.gz /tmp/W7LlGhaRlN/merge.3.b.vcf.gz The outputs differ: /<>/test/merge.3.out /<>/test/merge.3.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/W7LlGhaRlN/merge.3.a.vcf.gz /tmp/W7LlGhaRlN/merge.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.3.out /<>/test/merge.3.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/W7LlGhaRlN/merge.4.a.vcf.gz /tmp/W7LlGhaRlN/merge.4.b.vcf.gz The outputs differ: /<>/test/merge.4.out /<>/test/merge.4.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m id /tmp/W7LlGhaRlN/merge.4.a.vcf.gz /tmp/W7LlGhaRlN/merge.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.4.out /<>/test/merge.4.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/W7LlGhaRlN/gvcf.merge.1.vcf.gz /tmp/W7LlGhaRlN/gvcf.merge.2.vcf.gz /tmp/W7LlGhaRlN/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/W7LlGhaRlN/gvcf.merge.1.vcf.gz /tmp/W7LlGhaRlN/gvcf.merge.2.vcf.gz /tmp/W7LlGhaRlN/gvcf.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/W7LlGhaRlN/merge.gvcf.2.a.vcf.gz /tmp/W7LlGhaRlN/merge.gvcf.2.b.vcf.gz /tmp/W7LlGhaRlN/merge.gvcf.2.c.vcf.gz The outputs differ: /<>/test/merge.gvcf.2.out /<>/test/merge.gvcf.2.out.new .. failed ... test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/W7LlGhaRlN/merge.gvcf.2.a.vcf.gz /tmp/W7LlGhaRlN/merge.gvcf.2.b.vcf.gz /tmp/W7LlGhaRlN/merge.gvcf.2.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/merge.gvcf.2.out /<>/test/merge.gvcf.2.out.new .. failed ... test_vcf_merge: /<>/bcftools merge --no-version --gvcf - -i SRC:join /tmp/W7LlGhaRlN/merge.gvcf.3.a.vcf.gz /tmp/W7LlGhaRlN/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/W7LlGhaRlN/merge.gvcf.3.a.vcf.gz /tmp/W7LlGhaRlN/merge.gvcf.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/W7LlGhaRlN/merge.5.a.vcf.gz /tmp/W7LlGhaRlN/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/W7LlGhaRlN/merge.5.a.vcf.gz /tmp/W7LlGhaRlN/merge.5.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/W7LlGhaRlN/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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'%XRI\n' -i'XRI[*]>1111' /tmp/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/missing.vcf.gz The outputs differ: /<>/test/query.18.out /<>/test/query.18.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' The outputs differ: /<>/test/query.18.out /<>/test/query.18.out.new .. failed ... test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/W7LlGhaRlN/missing.vcf.gz The outputs differ: /<>/test/query.19.out /<>/test/query.19.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' The outputs differ: /<>/test/query.19.out /<>/test/query.19.out.new .. failed ... test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/W7LlGhaRlN/missing.vcf.gz The outputs differ: /<>/test/query.18.out /<>/test/query.18.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' The outputs differ: /<>/test/query.18.out /<>/test/query.18.out.new .. failed ... test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/W7LlGhaRlN/missing.vcf.gz The outputs differ: /<>/test/query.19.out /<>/test/query.19.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' The outputs differ: /<>/test/query.19.out /<>/test/query.19.out.new .. failed ... test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/W7LlGhaRlN/missing.vcf.gz The outputs differ: /<>/test/query.20.out /<>/test/query.20.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' The outputs differ: /<>/test/query.20.out /<>/test/query.20.out.new .. failed ... test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/W7LlGhaRlN/missing.vcf.gz The outputs differ: /<>/test/query.21.out /<>/test/query.21.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' The outputs differ: /<>/test/query.21.out /<>/test/query.21.out.new .. failed ... test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/W7LlGhaRlN/missing.vcf.gz The outputs differ: /<>/test/query.20.out /<>/test/query.20.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' The outputs differ: /<>/test/query.20.out /<>/test/query.20.out.new .. failed ... test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/W7LlGhaRlN/missing.vcf.gz The outputs differ: /<>/test/query.21.out /<>/test/query.21.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' The outputs differ: /<>/test/query.21.out /<>/test/query.21.out.new .. failed ... test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/W7LlGhaRlN/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/W7LlGhaRlN/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/W7LlGhaRlN/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/W7LlGhaRlN/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/missing.vcf.gz | /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/W7LlGhaRlN/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/W7LlGhaRlN/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/W7LlGhaRlN/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/missing.vcf.gz The outputs differ: /<>/test/query.32.out /<>/test/query.32.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/missing.vcf.gz | /<>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' The outputs differ: /<>/test/query.32.out /<>/test/query.32.out.new .. failed ... test_vcf_query: /<>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/W7LlGhaRlN/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz The outputs differ: /<>/test/query.40.out /<>/test/query.40.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' The outputs differ: /<>/test/query.40.out /<>/test/query.40.out.new .. failed ... test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/W7LlGhaRlN/view.filter.vcf.gz The outputs differ: /<>/test/query.41.out /<>/test/query.41.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' The outputs differ: /<>/test/query.41.out /<>/test/query.41.out.new .. failed ... test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/W7LlGhaRlN/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/filter.5.vcf.gz The outputs differ: /<>/test/query.43.out /<>/test/query.43.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/filter.5.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' The outputs differ: /<>/test/query.43.out /<>/test/query.43.out.new .. failed ... test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz The outputs differ: /<>/test/query.45.out /<>/test/query.45.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' The outputs differ: /<>/test/query.45.out /<>/test/query.45.out.new .. failed ... test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/W7LlGhaRlN/view.filter.vcf.gz The outputs differ: /<>/test/query.46.out /<>/test/query.46.out.new .. failed ... test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' The outputs differ: /<>/test/query.46.out /<>/test/query.46.out.new .. failed ... test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/W7LlGhaRlN/query.filter.4.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/query.filter.4.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_norm: /<>/bcftools norm --no-version -cx -f /<>/test/norm.fa /tmp/W7LlGhaRlN/norm.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -cx -f /<>/test/norm.fa /tmp/W7LlGhaRlN/norm.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/W7LlGhaRlN/norm.split.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.split.out /<>/test/norm.split.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/W7LlGhaRlN/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.split.out /<>/test/norm.split.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/W7LlGhaRlN/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/W7LlGhaRlN/norm.split.2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- -f /<>/test/norm.fa /tmp/W7LlGhaRlN/norm.split.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.split.and.norm.out /<>/test/norm.split.and.norm.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m- -f /<>/test/norm.fa /tmp/W7LlGhaRlN/norm.split.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.split.and.norm.out /<>/test/norm.split.and.norm.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/W7LlGhaRlN/norm.merge.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.merge.out /<>/test/norm.merge.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/W7LlGhaRlN/norm.merge.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.merge.out /<>/test/norm.merge.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/W7LlGhaRlN/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/W7LlGhaRlN/norm.merge.2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/W7LlGhaRlN/norm.merge.3.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.merge.3.out /<>/test/norm.merge.3.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/W7LlGhaRlN/norm.merge.3.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' The outputs differ: /<>/test/norm.merge.3.out /<>/test/norm.merge.3.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/W7LlGhaRlN/norm.merge.vcf.gz 2>/dev/null The outputs differ: /<>/test/norm.merge.strict.out /<>/test/norm.merge.strict.out.new .. failed ... test_vcf_norm: /<>/bcftools norm -Ob -m+ -s /tmp/W7LlGhaRlN/norm.merge.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/norm.merge.strict.out /<>/test/norm.merge.strict.out.new .. failed ... test_vcf_norm: /<>/bcftools norm --no-version -Nc s -f /<>/test/norm.fa /tmp/W7LlGhaRlN/norm.setref.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -Nc s -f /<>/test/norm.fa /tmp/W7LlGhaRlN/norm.setref.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.fa /tmp/W7LlGhaRlN/norm.telomere.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/W7LlGhaRlN/norm.telomere.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/W7LlGhaRlN/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d snps /tmp/W7LlGhaRlN/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/W7LlGhaRlN/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d indels /tmp/W7LlGhaRlN/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/W7LlGhaRlN/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d both /tmp/W7LlGhaRlN/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/W7LlGhaRlN/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d all /tmp/W7LlGhaRlN/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/W7LlGhaRlN/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /<>/bcftools norm -Ob -d none /tmp/W7LlGhaRlN/norm.rmdup.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/W7LlGhaRlN/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/W7LlGhaRlN/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/W7LlGhaRlN/view.vcf.gz -r20,Y .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/W7LlGhaRlN/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/W7LlGhaRlN/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/W7LlGhaRlN/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/W7LlGhaRlN/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/W7LlGhaRlN/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -p /tmp/W7LlGhaRlN/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/W7LlGhaRlN/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -P /tmp/W7LlGhaRlN/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/W7LlGhaRlN/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/W7LlGhaRlN/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/W7LlGhaRlN/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/W7LlGhaRlN/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/W7LlGhaRlN/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/W7LlGhaRlN/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/W7LlGhaRlN/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/W7LlGhaRlN/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/W7LlGhaRlN/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/W7LlGhaRlN/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/W7LlGhaRlN/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/W7LlGhaRlN/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/W7LlGhaRlN/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/W7LlGhaRlN/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/W7LlGhaRlN/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/W7LlGhaRlN/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/W7LlGhaRlN/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/W7LlGhaRlN/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asB /tmp/W7LlGhaRlN/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/W7LlGhaRlN/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/W7LlGhaRlN/view.vectors.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/W7LlGhaRlN/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/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/W7LlGhaRlN/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/W7LlGhaRlN/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/W7LlGhaRlN/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/W7LlGhaRlN/filter.2.vcf.gz 1:3062917-3157410 | /<>/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_view: /<>/bcftools view --no-version -H -C5:nonmajor /tmp/W7LlGhaRlN/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/W7LlGhaRlN/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/W7LlGhaRlN/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/W7LlGhaRlN/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/W7LlGhaRlN/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/W7LlGhaRlN/view.filter.annovar.vcf.gz .. ok test_vcf_call: /<>/bcftools call --no-version -mv /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv /<>/test/mpileup.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mg0 /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mg0 /<>/test/mpileup.vcf 2>/dev/null | /<>/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 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.X.vcf 2>/dev/null | /<>/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 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.X.vcf 2>/dev/null | /<>/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 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.X.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/W7LlGhaRlN/mpileup.tab.gz /<>/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/W7LlGhaRlN/mpileup.tab.gz /<>/test/mpileup.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv /<>/test/mpileup.c.vcf 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv /<>/test/mpileup.c.vcf 2>/dev/null | /<>/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 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.c.X.vcf 2>/dev/null | /<>/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 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.c.X.vcf 2>/dev/null | /<>/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 2>/dev/null .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.c.X.vcf 2>/dev/null | /<>/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'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'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'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'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'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'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'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'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'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'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' The outputs differ: /<>/test/filter.23.out /<>/test/filter.23.out.new .. failed ... test_vcf_filter: /<>/bcftools filter -Ob -i'AD[*]="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' The outputs differ: /<>/test/filter.23.out /<>/test/filter.23.out.new .. failed ... test_vcf_filter: /<>/bcftools filter -i'AD[0:0]=="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' The outputs differ: /<>/test/filter.24.out /<>/test/filter.24.out.new .. failed ... test_vcf_filter: /<>/bcftools filter -Ob -i'AD[0:0]=="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' The outputs differ: /<>/test/filter.24.out /<>/test/filter.24.out.new .. failed ... test_vcf_filter: /<>/bcftools filter -i'AD[0:0]!="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' The outputs differ: /<>/test/filter.25.out /<>/test/filter.25.out.new .. failed ... test_vcf_filter: /<>/bcftools filter -Ob -i'AD[0:0]!="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' The outputs differ: /<>/test/filter.25.out /<>/test/filter.25.out.new .. failed ... test_vcf_filter: /<>/bcftools filter -i'QUAL=="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS\t%QUAL\n' The outputs differ: /<>/test/filter.26.out /<>/test/filter.26.out.new .. failed ... test_vcf_filter: /<>/bcftools filter -Ob -i'QUAL=="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%QUAL\n' The outputs differ: /<>/test/filter.26.out /<>/test/filter.26.out.new .. failed ... test_vcf_sort: /<>/bcftools sort -m 0 /<>/test/sort.vcf | /<>/bcftools query -f '%CHROM\t%POS\n' Writing to /tmp/bcftools-sort.CACF17 Merging 15 temporary files Cleaning Done .. ok test_vcf_sort: /<>/bcftools sort -Ob -m 0 /<>/test/sort.vcf | /<>/bcftools view | /<>/bcftools query -f '%CHROM\t%POS\n' Writing to /tmp/bcftools-sort.ya2kPf Merging 15 temporary files Cleaning Done .. ok test_vcf_sort: /<>/bcftools sort -m 1000 /<>/test/sort.vcf | /<>/bcftools query -f '%CHROM\t%POS\n' Writing to /tmp/bcftools-sort.MUA1ch Merging 3 temporary files Cleaning Done .. ok test_vcf_sort: /<>/bcftools sort -Ob -m 1000 /<>/test/sort.vcf | /<>/bcftools view | /<>/bcftools query -f '%CHROM\t%POS\n' Writing to /tmp/bcftools-sort.L4NwJj Merging 3 temporary files Cleaning Done .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab /tmp/W7LlGhaRlN/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/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/W7LlGhaRlN/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/W7LlGhaRlN/regions.tab.gz /tmp/W7LlGhaRlN/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/W7LlGhaRlN/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/W7LlGhaRlN/regions.tab.gz /tmp/W7LlGhaRlN/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/W7LlGhaRlN/regions.bed /tmp/W7LlGhaRlN/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/W7LlGhaRlN/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/W7LlGhaRlN/regions.bed /tmp/W7LlGhaRlN/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/W7LlGhaRlN/regions.bed.gz /tmp/W7LlGhaRlN/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/W7LlGhaRlN/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/W7LlGhaRlN/regions.bed.gz /tmp/W7LlGhaRlN/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/W7LlGhaRlN/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/W7LlGhaRlN/annotate.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/W7LlGhaRlN/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate4.out /<>/test/annotate4.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/W7LlGhaRlN/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate4.out /<>/test/annotate4.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/W7LlGhaRlN/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/W7LlGhaRlN/annotate2.vcf.gz 2>/dev/null | /<>/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 2>/dev/null | /<>/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 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x FORMAT /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x FORMAT /<>/test/annotate3.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annots4.vcf.gz -c +INFO /tmp/W7LlGhaRlN/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate8.out /<>/test/annotate8.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annots4.vcf.gz -c +INFO /tmp/W7LlGhaRlN/annotate4.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate8.out /<>/test/annotate8.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate8.out /<>/test/annotate8.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate8.out /<>/test/annotate8.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annots10.tab.gz -h /<>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<>/test/annotate10.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate10.out /<>/test/annotate10.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annots10.tab.gz -h /<>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<>/test/annotate10.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate10.out /<>/test/annotate10.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/W7LlGhaRlN/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate11.out /<>/test/annotate11.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/W7LlGhaRlN/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate11.out /<>/test/annotate11.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<>/test/annotate2.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate11.out /<>/test/annotate11.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<>/test/annotate2.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ The outputs differ: /<>/test/annotate11.out /<>/test/annotate11.out.new .. failed ... test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/W7LlGhaRlN/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/W7LlGhaRlN/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/W7LlGhaRlN/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/W7LlGhaRlN/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/W7LlGhaRlN/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/W7LlGhaRlN/annotate2.vcf.gz 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +missing2ref --no-version /tmp/W7LlGhaRlN/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +missing2ref --no-version /tmp/W7LlGhaRlN/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/W7LlGhaRlN/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/W7LlGhaRlN/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/W7LlGhaRlN/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +setGT --no-version /tmp/W7LlGhaRlN/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/W7LlGhaRlN/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/W7LlGhaRlN/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-AN-AC --no-version /tmp/W7LlGhaRlN/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-AN-AC --no-version /tmp/W7LlGhaRlN/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +dosage /tmp/W7LlGhaRlN/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +dosage /tmp/W7LlGhaRlN/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixploidy --no-version /tmp/W7LlGhaRlN/fixploidy.vcf.gz -- -s /<>/test/fixploidy.samples -p /<>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixploidy --no-version /tmp/W7LlGhaRlN/fixploidy.bcf -- -s /<>/test/fixploidy.samples -p /<>/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/W7LlGhaRlN/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/W7LlGhaRlN/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/W7LlGhaRlN/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ Warning: PL tag not found in header, switching to GL The outputs differ: /<>/test/guess-ploidy.GL.out /<>/test/guess-ploidy.GL.out.new .. failed ... test_vcf_plugin: /<>/bcftools +guess-ploidy /tmp/W7LlGhaRlN/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ Warning: PL tag not found in header, switching to GL The outputs differ: /<>/test/guess-ploidy.GL.out /<>/test/guess-ploidy.GL.out.new .. failed ... test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/W7LlGhaRlN/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/W7LlGhaRlN/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/W7LlGhaRlN/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +tag2tag --no-version /tmp/W7LlGhaRlN/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/W7LlGhaRlN/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/W7LlGhaRlN/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/W7LlGhaRlN/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/W7LlGhaRlN/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/W7LlGhaRlN/view.vcf.gz -- -t AC -S /<>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/W7LlGhaRlN/view.bcf -- -t AC -S /<>/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/W7LlGhaRlN/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/W7LlGhaRlN/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/W7LlGhaRlN/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-tags --no-version /tmp/W7LlGhaRlN/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTisec /tmp/W7LlGhaRlN/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +trio-switch-rate /tmp/W7LlGhaRlN/trio.vcf.gz -- -p /<>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +trio-switch-rate /tmp/W7LlGhaRlN/trio.bcf -- -p /<>/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +ad-bias /tmp/W7LlGhaRlN/ad-bias.vcf.gz -- -s /<>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +ad-bias /tmp/W7LlGhaRlN/ad-bias.bcf -- -s /<>/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +af-dist /tmp/W7LlGhaRlN/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +af-dist /tmp/W7LlGhaRlN/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixref /tmp/W7LlGhaRlN/fixref.2a.vcf.gz -- -f /<>/test/norm.fa -i /tmp/W7LlGhaRlN/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fixref /tmp/W7LlGhaRlN/fixref.2a.bcf -- -f /<>/test/norm.fa -i /tmp/W7LlGhaRlN/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-from-fasta /tmp/W7LlGhaRlN/aa.vcf.gz -- -f /<>/test/aa.fa -c AA -h /<>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-from-fasta /tmp/W7LlGhaRlN/aa.bcf -- -f /<>/test/aa.fa -c AA -h /<>/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-from-fasta /tmp/W7LlGhaRlN/ref.vcf.gz -- -f /<>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +fill-from-fasta /tmp/W7LlGhaRlN/ref.bcf -- -f /<>/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/W7LlGhaRlN/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/W7LlGhaRlN/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/W7LlGhaRlN/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/W7LlGhaRlN/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/W7LlGhaRlN/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +GTsubset --no-version /tmp/W7LlGhaRlN/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/W7LlGhaRlN/mendelian.vcf.gz -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/W7LlGhaRlN/mendelian.bcf -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/W7LlGhaRlN/mendelian.vcf.gz -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/W7LlGhaRlN/mendelian.bcf -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/W7LlGhaRlN/mendelian.vcf.gz -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /<>/bcftools +mendelian /tmp/W7LlGhaRlN/mendelian.bcf -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/W7LlGhaRlN/concat.1.a.vcf.gz /tmp/W7LlGhaRlN/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/W7LlGhaRlN/concat.1.a.vcf.gz /tmp/W7LlGhaRlN/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/W7LlGhaRlN/concat.1.a.bcf /tmp/W7LlGhaRlN/concat.1.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/W7LlGhaRlN/concat.1.a.bcf /tmp/W7LlGhaRlN/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/W7LlGhaRlN/concat.2.a.vcf.gz /tmp/W7LlGhaRlN/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/W7LlGhaRlN/concat.2.a.vcf.gz /tmp/W7LlGhaRlN/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/W7LlGhaRlN/concat.2.a.bcf /tmp/W7LlGhaRlN/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/W7LlGhaRlN/concat.2.a.bcf /tmp/W7LlGhaRlN/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/W7LlGhaRlN/concat.2.a.vcf.gz /tmp/W7LlGhaRlN/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/W7LlGhaRlN/concat.2.a.vcf.gz /tmp/W7LlGhaRlN/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/W7LlGhaRlN/concat.2.a.bcf /tmp/W7LlGhaRlN/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/W7LlGhaRlN/concat.2.a.bcf /tmp/W7LlGhaRlN/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/W7LlGhaRlN/concat.3.a.vcf.gz /tmp/W7LlGhaRlN/concat.3.b.vcf.gz /tmp/W7LlGhaRlN/concat.3.0.vcf.gz /tmp/W7LlGhaRlN/concat.3.c.vcf.gz /tmp/W7LlGhaRlN/concat.3.d.vcf.gz /tmp/W7LlGhaRlN/concat.3.e.vcf.gz /tmp/W7LlGhaRlN/concat.3.f.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/W7LlGhaRlN/concat.3.a.vcf.gz /tmp/W7LlGhaRlN/concat.3.b.vcf.gz /tmp/W7LlGhaRlN/concat.3.0.vcf.gz /tmp/W7LlGhaRlN/concat.3.c.vcf.gz /tmp/W7LlGhaRlN/concat.3.d.vcf.gz /tmp/W7LlGhaRlN/concat.3.e.vcf.gz /tmp/W7LlGhaRlN/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/W7LlGhaRlN/concat.3.a.bcf /tmp/W7LlGhaRlN/concat.3.b.bcf /tmp/W7LlGhaRlN/concat.3.0.bcf /tmp/W7LlGhaRlN/concat.3.c.bcf /tmp/W7LlGhaRlN/concat.3.d.bcf /tmp/W7LlGhaRlN/concat.3.e.bcf /tmp/W7LlGhaRlN/concat.3.f.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/W7LlGhaRlN/concat.3.a.bcf /tmp/W7LlGhaRlN/concat.3.b.bcf /tmp/W7LlGhaRlN/concat.3.0.bcf /tmp/W7LlGhaRlN/concat.3.c.bcf /tmp/W7LlGhaRlN/concat.3.d.bcf /tmp/W7LlGhaRlN/concat.3.e.bcf /tmp/W7LlGhaRlN/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 163509950 .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/W7LlGhaRlN/naive_concat.0.bcf /tmp/W7LlGhaRlN/naive_concat.1.bcf /tmp/W7LlGhaRlN/naive_concat.2.bcf /tmp/W7LlGhaRlN/naive_concat.3.bcf /tmp/W7LlGhaRlN/naive_concat.4.bcf /tmp/W7LlGhaRlN/naive_concat.5.bcf /tmp/W7LlGhaRlN/naive_concat.6.bcf /tmp/W7LlGhaRlN/naive_concat.7.bcf /tmp/W7LlGhaRlN/naive_concat.8.bcf /tmp/W7LlGhaRlN/naive_concat.9.bcf | /<>/bcftools view -H .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/W7LlGhaRlN/naive_concat.0.vcf.gz /tmp/W7LlGhaRlN/naive_concat.1.vcf.gz /tmp/W7LlGhaRlN/naive_concat.2.vcf.gz /tmp/W7LlGhaRlN/naive_concat.3.vcf.gz /tmp/W7LlGhaRlN/naive_concat.4.vcf.gz /tmp/W7LlGhaRlN/naive_concat.5.vcf.gz /tmp/W7LlGhaRlN/naive_concat.6.vcf.gz /tmp/W7LlGhaRlN/naive_concat.7.vcf.gz /tmp/W7LlGhaRlN/naive_concat.8.vcf.gz /tmp/W7LlGhaRlN/naive_concat.9.vcf.gz | /<>/bcftools view -H .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/W7LlGhaRlN/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W7LlGhaRlN/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/W7LlGhaRlN/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W7LlGhaRlN/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/W7LlGhaRlN/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W7LlGhaRlN/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/W7LlGhaRlN/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W7LlGhaRlN/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/W7LlGhaRlN/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W7LlGhaRlN/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/W7LlGhaRlN/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W7LlGhaRlN/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/W7LlGhaRlN/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W7LlGhaRlN/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/W7LlGhaRlN/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W7LlGhaRlN/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/W7LlGhaRlN/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W7LlGhaRlN/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/W7LlGhaRlN/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W7LlGhaRlN/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/W7LlGhaRlN/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W7LlGhaRlN/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/W7LlGhaRlN/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/W7LlGhaRlN/empty.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/W7LlGhaRlN/rename.map -Ov /tmp/W7LlGhaRlN/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/W7LlGhaRlN/rename.map -Ob /tmp/W7LlGhaRlN/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/W7LlGhaRlN/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/W7LlGhaRlN/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/W7LlGhaRlN/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/convert.vcf.gz | /<>/bcftools convert -g -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/W7LlGhaRlN/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/convert.vcf.gz | /<>/bcftools convert -g .,- 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/W7LlGhaRlN/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/W7LlGhaRlN/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/W7LlGhaRlN/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/W7LlGhaRlN/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/W7LlGhaRlN/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/check.vcf.gz | /<>/bcftools convert -g -,. --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom /tmp/W7LlGhaRlN/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/check.vcf.gz | /<>/bcftools convert -g .,- --chrom 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/W7LlGhaRlN/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/check.vcf.gz | /<>/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/W7LlGhaRlN/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/W7LlGhaRlN/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/convert.vcf.gz | /<>/bcftools convert -h -,.,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/W7LlGhaRlN/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/convert.vcf.gz | /<>/bcftools convert -h .,-,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/W7LlGhaRlN/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/convert.vcf.gz | /<>/bcftools convert -h .,.,- 2>/dev/null .. ok test_vcf_convert_hls2vcf: /<>/bcftools convert -H /<>/test/convert.hls.gt.hap,/<>/test/convert.hls.gt.legend,/<>/test/convert.hls.gt.samples 2>/dev/null | 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 2>/dev/null | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples 2>/dev/null | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples -Ou 2>/dev/null | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/W7LlGhaRlN/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/convert.vcf.gz | /<>/bcftools convert --hapsample -,. 2>/dev/null .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/W7LlGhaRlN/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/convert.vcf.gz | /<>/bcftools convert --hapsample .,- 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools convert --no-version --gvcf2vcf -f /<>/test/gvcf.fa /tmp/W7LlGhaRlN/convert.gvcf.vcf.gz 2>/dev/null .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/W7LlGhaRlN/convert.gvcf.vcf.gz | /<>/bcftools convert --gvcf2vcf -f /<>/test/gvcf.fa 2>/dev/null | 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 2>/dev/null .. ok test_vcf_convert_tsv2vcf: /<>/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.23andme 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/W7LlGhaRlN/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/W7LlGhaRlN/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/W7LlGhaRlN/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/W7LlGhaRlN/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/W7LlGhaRlN/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/W7LlGhaRlN/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/W7LlGhaRlN/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/W7LlGhaRlN/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/W7LlGhaRlN/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/W7LlGhaRlN/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab -c /tmp/W7LlGhaRlN/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/W7LlGhaRlN/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/W7LlGhaRlN/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 2>/dev/null .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/W7LlGhaRlN/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/W7LlGhaRlN/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/W7LlGhaRlN/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/W7LlGhaRlN/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/W7LlGhaRlN/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 2>/dev/null .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/W7LlGhaRlN/empty.vcf.gz -f /<>/test/consensus.fa 2>/dev/null .. 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 2>/dev/null | 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 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -b /tmp/W7LlGhaRlN/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/W7LlGhaRlN/mpileup.bam.urllist 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -b /tmp/W7LlGhaRlN/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/W7LlGhaRlN/mpileup.cram.urllist 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/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 2>/dev/null | 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 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... 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 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/mpileup.11.out /<>/test/mpileup/mpileup.11.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa /<>/test/mpileup/indel-AD.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/indel-AD.1.out /<>/test/mpileup/indel-AD.1.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa -Ob /<>/test/mpileup/indel-AD.1.bam 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/indel-AD.1.out /<>/test/mpileup/indel-AD.1.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa /<>/test/mpileup/indel-AD.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/indel-AD.1.out /<>/test/mpileup/indel-AD.1.out.new .. failed ... test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa -Ob /<>/test/mpileup/indel-AD.1.cram 2>/dev/null | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference The outputs differ: /<>/test/mpileup/indel-AD.1.out /<>/test/mpileup/indel-AD.1.out.new .. failed ... 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' Parsing /<>/test/csq.gff3 ... Indexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000436063/ENST00000436063.gff ... Indexed 1 transcripts, 7 exons, 7 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000373833/ENST00000373833.gff ... Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000373833/ENST00000373833.gff ... Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000381157/ENST00000381157.gff ... Indexed 1 transcripts, 6 exons, 6 CDSs, 0 UTRs Calling... Warning: Skipping site with non-diploid/non-haploid genotypes at X:31180 C>T .. 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' Parsing /<>/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000413103/ENST00000413103.gff ... Indexed 1 transcripts, 2 exons, 0 CDSs, 0 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000295641/ENST00000295641.gff ... Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000295641/ENST00000295641.gff ... Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000256452/ENST00000256452.gff ... Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000479739/ENST00000479739.gff ... Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000479739/ENST00000479739.gff ... Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000536784/ENST00000536784.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000536784/ENST00000536784.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000542803/ENST00000542803.gff ... Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000542803/ENST00000542803.gff ... Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000557788/ENST00000557788.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000624631/ENST00000624631.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. 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' Parsing /<>/test/csq/ENSG00000173376/ENSG00000173376.gff ... Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000543077/ENST00000543077.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000543077/ENST00000543077.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000520795/ENST00000520795.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000520795/ENST00000520795.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000409523/ENST00000409523.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000519442/ENST00000519442.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000520868/ENST00000520868.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000420670/ENST00000420670.gff ... Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000382647/ENST00000382647.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000573314/ENST00000573314.gff ... Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000573314/ENST00000573314.gff ... Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000368801/ENST00000368801.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000375992/ENST00000375992.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000593942/ENST00000593942.gff ... Indexed 1 transcripts, 7 exons, 4 CDSs, 5 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000528237/ENST00000528237.gff ... Indexed 1 transcripts, 7 exons, 6 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000329454/ENST00000329454.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000329454/ENST00000329454.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000227471/ENST00000227471.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000271583/ENST00000271583.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000301246/ENST00000301246.gff ... Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000410009/ENST00000410009.gff ... Indexed 1 transcripts, 6 exons, 6 CDSs, 2 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000390520/ENST00000390520.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 0 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000318249/ENST00000318249.gff ... Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000318249/ENST00000318249.gff ... Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000545279/ENST00000545279.gff ... Indexed 1 transcripts, 9 exons, 7 CDSs, 4 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000448695/ENST00000448695.gff ... Indexed 1 transcripts, 26 exons, 26 CDSs, 1 UTRs Calling... .. 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' Parsing /<>/test/csq/ENST00000357367/ENST00000357367.gff ... Indexed 1 transcripts, 4 exons, 3 CDSs, 3 UTRs Calling... .. ok Number of tests: total .. 792 passed .. 690 failed .. 102 Makefile:246: recipe for target 'test-plugins' failed make[1]: *** [test-plugins] Error 1 make[1]: Leaving directory '/<>' dh_auto_test: make -j4 -O test VERBOSE=1 returned exit code 2 debian/rules:7: recipe for target 'build-arch' failed make: *** [build-arch] Error 25 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20190128-1026 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 22392 Build-Time: 94 Distribution: bionic Fail-Stage: build Host Architecture: i386 Install-Time: 18 Job: bcftools_1.7-2.dsc Machine Architecture: amd64 Package: bcftools Package-Time: 112 Source-Version: 1.7-2 Space: 22392 Status: attempted Version: 1.7-2 -------------------------------------------------------------------------------- Finished at 20190128-1026 Build needed 00:01:52, 22392k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-16009151 Scanning for processes to kill in build PACKAGEBUILD-16009151