I: pbuilder: network access will be disabled during build I: Current time: Sat Jul 18 13:30:11 +14 2020 I: pbuilder-time-stamp: 1595028611 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bcftools_1.9-1.dsc] I: copying [./bcftools_1.9.orig.tar.gz] I: copying [./bcftools_1.9-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Sep 5 04:47:28 2018 +14 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_1.9-1.dsc dpkg-source: info: extracting bcftools in bcftools-1.9 dpkg-source: info: unpacking bcftools_1.9.orig.tar.gz dpkg-source: info: unpacking bcftools_1.9-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying skip_new_test_failing_on_32bit.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/14432/tmp/hooks/D01_modify_environment starting debug: Running on wbq0. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/14432/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/14432/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=9975ef5bd28b4242996926706fda3840 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=14432 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.n6w9MFigbR/pbuilderrc_4v8R --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.n6w9MFigbR/b2 --logfile b2/build.log bcftools_1.9-1.dsc' SUDO_GID=115 SUDO_UID=111 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:8000/ I: uname -a Linux i-capture-the-hostname 4.19.0-9-armmp #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) armv7l GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 22432 Mar 1 2019 cat -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash -rwxr-xr-x 1 root root 71648 Mar 1 2019 date -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd -rwxr-xr-x 1 root root 55672 Mar 1 2019 df -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir -rwxr-xr-x 1 root root 54872 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 18260 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 23 09:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 6 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln -rwxr-xr-x 1 root root 34932 Jul 27 2018 login -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 10 2019 more -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 84284 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 18 13:31 sh -> bash lrwxrwxrwx 1 root root 4 Jul 16 22:27 sh.distrib -> dash -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty -rwsr-xr-x 1 root root 42472 Jan 10 2019 su -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch -rwxr-xr-x 1 root root 18260 Mar 1 2019 true -rwxr-xr-x 1 root root 9636 Apr 23 09:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/14432/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.5-3); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on libio-pty-perl; however: Package libio-pty-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libbz2-dev{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu63{a} libio-pty-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 59 newly installed, 0 to remove and 0 not upgraded. Need to get 28.3 MB of archives. After unpacking 83.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 24 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 30 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 31 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main armhf libbz2-dev armhf 1.0.6-9.2~deb10u1 [28.8 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3 [62.3 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3 [119 kB] Get: 38 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 39 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3 [323 kB] Get: 40 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3 [137 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1+deb10u1 [67.4 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libsasl2-2 armhf 2.1.27+dfsg-1+deb10u1 [98.9 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libldap-2.4-2 armhf 2.4.47+dfsg-3+deb10u2 [202 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libnghttp2-14 armhf 1.36.0-2+deb10u1 [74.4 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libpsl5 armhf 0.20.2-2 [52.4 kB] Get: 47 http://deb.debian.org/debian buster/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.9 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libssh2-1 armhf 1.8.0-2.1 [129 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libcurl3-gnutls armhf 7.64.0-4+deb10u1 [295 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libdeflate0 armhf 1.2-1 [46.4 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libgslcblas0 armhf 2.5+dfsg-6 [79.1 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libgsl23 armhf 2.5+dfsg-6 [718 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libgsl-dev armhf 2.5+dfsg-6 [903 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libhts2 armhf 1.9-11 [261 kB] Get: 55 http://deb.debian.org/debian buster/main armhf liblzma-dev armhf 5.2.4-1 [204 kB] Get: 56 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] Get: 57 http://deb.debian.org/debian buster/main armhf libhts-dev armhf 1.9-11 [4289 kB] Get: 58 http://deb.debian.org/debian buster/main armhf libio-pty-perl armhf 1:1.08-1.1+b5 [32.9 kB] Get: 59 http://deb.debian.org/debian buster/main armhf tabix armhf 1.9-11 [263 kB] Fetched 28.3 MB in 17s (1637 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../11-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. 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Setting up libssl1.1:armhf (1.1.1d-0+deb10u3) ... Setting up libnghttp2-14:armhf (1.36.0-2+deb10u1) ... Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up libdeflate0:armhf (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u2) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up libkrb5support0:armhf (1.17-3) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ... Setting up libgsl23:armhf (2.5+dfsg-6) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:armhf (1.17-3) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up liblzma-dev:armhf (5.2.4-1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libssh2-1:armhf (1.8.0-2.1) ... Setting up libkrb5-3:armhf (1.17-3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libbz2-dev:armhf (1.0.6-9.2~deb10u1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libgsl-dev (2.5+dfsg-6) ... Setting up libtool (2.4.6-9) ... Setting up libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u2) ... Setting up m4 (1.4.18-2) ... Setting up bsdmainutils (11.1.2+b1) ... 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 libgssapi-krb5-2:armhf (1.17-3) ... Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libcurl3-gnutls:armhf (7.64.0-4+deb10u1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up tabix (1.9-11) ... Setting up libhts2:armhf (1.9-11) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:armhf (1.9-11) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/bcftools-1.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.9-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean rm -f config.mk && touch config.mk dh clean dh_auto_clean make -j4 distclean make[1]: Entering directory '/build/bcftools-1.9' rm -f test/*.o test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f gmon.out *.o *~ bcftools version.h plugins/*.so plugins/*.P rm -rf *.dSYM plugins/*.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[1]: Leaving directory '/build/bcftools-1.9' dh_clean debian/rules build dh build dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/bcftools-1.9' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: 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:94: the top level configure.ac:94: 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:94: the top level configure.ac:94: 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:94: the top level make[1]: Leaving directory '/build/bcftools-1.9' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bcftools-1.9' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/arm-linux-gnueabihf/bcftools ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/arm-linux-gnueabihf/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 grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 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 '/build/bcftools-1.9' dh_auto_build make -j4 make[1]: Entering directory '/build/bcftools-1.9' echo '#define BCFTOOLS_VERSION "1.9"' > version.h gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c vcfmerge.c: In function 'merge_vcf': vcfmerge.c:2334:46: warning: '__builtin___snprintf_chk' output may be truncated before the last format character [-Wformat-truncation=] char buf[10]; snprintf(buf,10,"%d",i+1); ^ In file included from /usr/include/stdio.h:873, from vcfmerge.c:25: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 10 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/arm-linux-gnueabihf/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split.so version.c plugins/split.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -ldl -ldl gcc -rdynamic -pthread -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 '/build/bcftools-1.9' dh_auto_test make -j4 test VERBOSE=1 make[1]: Entering directory '/build/bcftools-1.9' ./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/RsCoEawrJC/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/RsCoEawrJC/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/RsCoEawrJC/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/RsCoEawrJC/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/RsCoEawrJC/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/RsCoEawrJC/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/RsCoEawrJC/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/RsCoEawrJC/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/RsCoEawrJC/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/RsCoEawrJC/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/RsCoEawrJC/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/RsCoEawrJC/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/RsCoEawrJC/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/RsCoEawrJC/empty.bcf .. ok test_vcf_check: /build/bcftools-1.9/bcftools stats -s - /tmp/RsCoEawrJC/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/bcftools-1.9/misc/plot-vcfstats -m /tmp/RsCoEawrJC/check.1.chk /tmp/RsCoEawrJC/check.2.chk /tmp/RsCoEawrJC/check.3.chk /tmp/RsCoEawrJC/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.9/bcftools stats -s - /tmp/RsCoEawrJC/stats.a.vcf.gz /tmp/RsCoEawrJC/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.9/bcftools stats -s B /tmp/RsCoEawrJC/stats.a.vcf.gz /tmp/RsCoEawrJC/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.9/bcftools stats -s - /tmp/RsCoEawrJC/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -n =2 /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -Ob -n =2 /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -n =2 -c both /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -Ob -n =2 -c both /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -n =2 -c any /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -Ob -n =2 -c any /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -C -c any /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -Ob -C -c any /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /build/bcftools-1.9/bcftools isec --no-version -T /tmp/RsCoEawrJC/isec.tab.gz /tmp/RsCoEawrJC/isec.a.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /build/bcftools-1.9/bcftools isec -Ob -T /tmp/RsCoEawrJC/isec.tab.gz /tmp/RsCoEawrJC/isec.a.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge --no-version --force-samples /tmp/RsCoEawrJC/merge.a.vcf.gz /tmp/RsCoEawrJC/merge.b.vcf.gz /tmp/RsCoEawrJC/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples /tmp/RsCoEawrJC/merge.a.vcf.gz /tmp/RsCoEawrJC/merge.b.vcf.gz /tmp/RsCoEawrJC/merge.c.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge --no-version --force-samples -Fx /tmp/RsCoEawrJC/merge.a.vcf.gz /tmp/RsCoEawrJC/merge.b.vcf.gz /tmp/RsCoEawrJC/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -Fx /tmp/RsCoEawrJC/merge.a.vcf.gz /tmp/RsCoEawrJC/merge.b.vcf.gz /tmp/RsCoEawrJC/merge.c.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge --no-version --force-samples -0 /tmp/RsCoEawrJC/merge.a.vcf.gz /tmp/RsCoEawrJC/merge.b.vcf.gz /tmp/RsCoEawrJC/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -0 /tmp/RsCoEawrJC/merge.a.vcf.gz /tmp/RsCoEawrJC/merge.b.vcf.gz /tmp/RsCoEawrJC/merge.c.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge --no-version --force-samples -m none /tmp/RsCoEawrJC/merge.2.a.vcf.gz /tmp/RsCoEawrJC/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -m none /tmp/RsCoEawrJC/merge.2.a.vcf.gz /tmp/RsCoEawrJC/merge.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge --no-version --force-samples -m both /tmp/RsCoEawrJC/merge.2.a.vcf.gz /tmp/RsCoEawrJC/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -m both /tmp/RsCoEawrJC/merge.2.a.vcf.gz /tmp/RsCoEawrJC/merge.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge --no-version --force-samples -m all /tmp/RsCoEawrJC/merge.2.a.vcf.gz /tmp/RsCoEawrJC/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -m all /tmp/RsCoEawrJC/merge.2.a.vcf.gz /tmp/RsCoEawrJC/merge.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/RsCoEawrJC/merge.3.a.vcf.gz /tmp/RsCoEawrJC/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/RsCoEawrJC/merge.3.a.vcf.gz /tmp/RsCoEawrJC/merge.3.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge --no-version --force-samples -m id /tmp/RsCoEawrJC/merge.4.a.vcf.gz /tmp/RsCoEawrJC/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -m id /tmp/RsCoEawrJC/merge.4.a.vcf.gz /tmp/RsCoEawrJC/merge.4.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge --no-version --gvcf - /tmp/RsCoEawrJC/gvcf.merge.1.vcf.gz /tmp/RsCoEawrJC/gvcf.merge.2.vcf.gz /tmp/RsCoEawrJC/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/RsCoEawrJC/gvcf.merge.1.vcf.gz /tmp/RsCoEawrJC/gvcf.merge.2.vcf.gz /tmp/RsCoEawrJC/gvcf.merge.3.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge --no-version --gvcf - /tmp/RsCoEawrJC/merge.gvcf.2.a.vcf.gz /tmp/RsCoEawrJC/merge.gvcf.2.b.vcf.gz /tmp/RsCoEawrJC/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/RsCoEawrJC/merge.gvcf.2.a.vcf.gz /tmp/RsCoEawrJC/merge.gvcf.2.b.vcf.gz /tmp/RsCoEawrJC/merge.gvcf.2.c.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge --no-version --gvcf - -i SRC:join /tmp/RsCoEawrJC/merge.gvcf.3.a.vcf.gz /tmp/RsCoEawrJC/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --gvcf - -i SRC:join /tmp/RsCoEawrJC/merge.gvcf.3.a.vcf.gz /tmp/RsCoEawrJC/merge.gvcf.3.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge --no-version /tmp/RsCoEawrJC/merge.5.a.vcf.gz /tmp/RsCoEawrJC/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob /tmp/RsCoEawrJC/merge.5.a.vcf.gz /tmp/RsCoEawrJC/merge.5.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/bcftools-1.9/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/RsCoEawrJC/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.vectors.vcf.gz | /build/bcftools-1.9/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: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/RsCoEawrJC/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/RsCoEawrJC/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/RsCoEawrJC/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/RsCoEawrJC/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/RsCoEawrJC/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.2.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%LINE' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%LINE' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/RsCoEawrJC/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter-type.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/RsCoEawrJC/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter-type.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/RsCoEawrJC/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter-type.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/RsCoEawrJC/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter-type.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/bcftools-1.9/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/RsCoEawrJC/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/filter-missing-floats.vcf.gz | /build/bcftools-1.9/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: /build/bcftools-1.9/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/RsCoEawrJC/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/filter-missing-floats.vcf.gz | /build/bcftools-1.9/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: /build/bcftools-1.9/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/RsCoEawrJC/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.2.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/RsCoEawrJC/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/filter.5.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/RsCoEawrJC/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/filter.5.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/RsCoEawrJC/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.3.vcf.gz | /build/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/RsCoEawrJC/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.3.vcf.gz | /build/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/RsCoEawrJC/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.3.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/RsCoEawrJC/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.4.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.9/test/query.56.out' /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.9/test/query.56.out' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/RsCoEawrJC/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.5.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/RsCoEawrJC/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.5.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' .. ok test_vcf_query: /build/bcftools-1.9/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/RsCoEawrJC/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.5.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -cx -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -cx -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -m- /tmp/RsCoEawrJC/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m- /tmp/RsCoEawrJC/norm.split.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -m- /tmp/RsCoEawrJC/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m- /tmp/RsCoEawrJC/norm.split.2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -m- -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m- -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.split.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -m+ /tmp/RsCoEawrJC/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/RsCoEawrJC/norm.merge.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -m+ /tmp/RsCoEawrJC/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/RsCoEawrJC/norm.merge.2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -m+ /tmp/RsCoEawrJC/norm.merge.3.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/RsCoEawrJC/norm.merge.3.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -m+ -s /tmp/RsCoEawrJC/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m+ -s /tmp/RsCoEawrJC/norm.merge.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -Nc s -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.setref.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -Nc s -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.setref.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.telomere.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.telomere.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -d snps /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d snps /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -d indels /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d indels /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -d both /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d both /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -d all /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d all /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm --no-version -d none /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d none /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -f PASS -Xks NA00003 /tmp/RsCoEawrJC/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -f PASS -Xks NA00003 /tmp/RsCoEawrJC/view.vcf.gz -r20,Y | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -xs NA00003 /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -xs NA00003 /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -p /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -p /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -P /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -P /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -Hu /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -GVsnps /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -GVsnps /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -s ^NA00003 /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -s ^NA00003 /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version /tmp/RsCoEawrJC/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.omitgenotypes.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -G /tmp/RsCoEawrJC/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -G /tmp/RsCoEawrJC/view.omitgenotypes.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -HG /tmp/RsCoEawrJC/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -a /tmp/RsCoEawrJC/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -a /tmp/RsCoEawrJC/many.alleles.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -asA /tmp/RsCoEawrJC/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -asA /tmp/RsCoEawrJC/view.vectors.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -asB /tmp/RsCoEawrJC/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -asB /tmp/RsCoEawrJC/view.vectors.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -asA /tmp/RsCoEawrJC/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -asA /tmp/RsCoEawrJC/view.vectors.2.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i'TXT0="text"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -T /build/bcftools-1.9/test/view.chrs.tab /tmp/RsCoEawrJC/view.chrs.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -T /build/bcftools-1.9/test/view.chrs.tab /tmp/RsCoEawrJC/view.chrs.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -i 'POS>=3062917' /tmp/RsCoEawrJC/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -i 'POS>=3062917' /tmp/RsCoEawrJC/filter.2.vcf.gz 1:3062917-3157410 | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S. -e'TXT0="text"' /build/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S. -e'TXT0="text"' /build/bcftools-1.9/test/view.filter.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-1.9/test/view.filter.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-1.9/test/view.filter.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-1.9/test/view.filter.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-1.9/test/view.filter.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S. -e'FMT/STR="XX"' /build/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/bcftools-1.9/test/view.filter.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -C5:nonmajor /tmp/RsCoEawrJC/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -c6:nonmajor /tmp/RsCoEawrJC/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -q0.3:major /tmp/RsCoEawrJC/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/RsCoEawrJC/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/RsCoEawrJC/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/RsCoEawrJC/view.filter.annovar.vcf.gz .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -mv /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -mv /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -mg0 /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -mg0 /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.samples /build/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.samples /build/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.ped /build/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.ped /build/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.2.samples /build/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.2.samples /build/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.9/bcftools call --no-version -mA -C alleles -T /tmp/RsCoEawrJC/mpileup.tab.gz /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call_cAls: /build/bcftools-1.9/bcftools call -Ob -mA -C alleles -T /tmp/RsCoEawrJC/mpileup.tab.gz /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -cv /build/bcftools-1.9/test/mpileup.c.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -cv /build/bcftools-1.9/test/mpileup.c.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.samples /build/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.samples /build/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.ped /build/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.ped /build/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.2.samples /build/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.2.samples /build/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -mx -g2 -G2 /build/bcftools-1.9/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -mx -g2 -G2 /build/bcftools-1.9/test/filter.1.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-1.9/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'INFO/DP=19' /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'INFO/DP=19' -s XX /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'INFO/DP=19' -s XX -mx /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' -s XX /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'ALT="."' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'ALT="."' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/bcftools-1.9/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/bcftools-1.9/test/filter.4.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/bcftools-1.9/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/bcftools-1.9/test/filter.4.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="A"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="A"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="RR"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="RR"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="RA"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="RA"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="AR"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="AR"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="AA"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="AA"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="aA"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="aA"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="Aa"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="Aa"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="HOM"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="HOM"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="HET"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="HET"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="HAP"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="HAP"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'AD[:1]=11' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'AD[:1]=11' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'AD[1:]=11' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'AD[1:]=11' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'FR[0:1]=11' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'FR[0:1]=11' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'AD[*]="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'AD[*]="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'AD[0:0]=="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'AD[0:0]=="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'AD[0:0]!="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'AD[0:0]!="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'QUAL=="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'QUAL=="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'N_PASS(DP>32)=1' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'F_PASS(DP>32)=0.5' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_sort: /build/bcftools-1.9/bcftools sort -m 0 /build/bcftools-1.9/test/sort.vcf | /build/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.BAdACk Merging 17 temporary files Cleaning Done .. ok test_vcf_sort: /build/bcftools-1.9/bcftools sort -Ob -m 0 /build/bcftools-1.9/test/sort.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.V42Xro Merging 17 temporary files Cleaning Done .. ok test_vcf_sort: /build/bcftools-1.9/bcftools sort -m 1000 /build/bcftools-1.9/test/sort.vcf | /build/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.d0malH Merging 3 temporary files Cleaning Done .. ok test_vcf_sort: /build/bcftools-1.9/bcftools sort -Ob -m 1000 /build/bcftools-1.9/test/sort.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.KomGgU Merging 3 temporary files Cleaning Done .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.9/test/regions.tab /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.9/test/regions.tab .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/bcftools-1.9/test/regions.tab /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/RsCoEawrJC/regions.tab.gz /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/RsCoEawrJC/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/RsCoEawrJC/regions.tab.gz /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/RsCoEawrJC/regions.bed /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/RsCoEawrJC/regions.bed .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/RsCoEawrJC/regions.bed /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/RsCoEawrJC/regions.bed.gz /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/RsCoEawrJC/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/RsCoEawrJC/regions.bed.gz /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annotate.tab.gz -h /build/bcftools-1.9/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-1.9/test/annotate.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annotate.tab.gz -h /build/bcftools-1.9/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-1.9/test/annotate.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annotate2.tab.gz -h /build/bcftools-1.9/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-1.9/test/annotate.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annotate2.tab.gz -h /build/bcftools-1.9/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-1.9/test/annotate.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/RsCoEawrJC/annotate.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/RsCoEawrJC/annotate.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-1.9/test/annotate3.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-1.9/test/annotate3.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -x FORMAT /build/bcftools-1.9/test/annotate3.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -x FORMAT /build/bcftools-1.9/test/annotate3.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots4.vcf.gz -c +INFO /tmp/RsCoEawrJC/annotate4.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots4.vcf.gz -c +INFO /tmp/RsCoEawrJC/annotate4.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots4.tab.gz -h /build/bcftools-1.9/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-1.9/test/annotate4.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots4.tab.gz -h /build/bcftools-1.9/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-1.9/test/annotate4.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots10.tab.gz -h /build/bcftools-1.9/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-1.9/test/annotate10.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots10.tab.gz -h /build/bcftools-1.9/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-1.9/test/annotate10.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-1.9/test/annotate2.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-1.9/test/annotate2.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots11.vcf.gz -c FMT /tmp/RsCoEawrJC/annotate11.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots11.vcf.gz -c FMT /tmp/RsCoEawrJC/annotate11.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +missing2ref --no-version /tmp/RsCoEawrJC/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +missing2ref --no-version /tmp/RsCoEawrJC/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/build/bcftools-1.9/test/setGT.samples.txt]="het"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/setGT.2.bcf -- -t q -n . -i 'GT[@/build/bcftools-1.9/test/setGT.samples.txt]="het"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/build/bcftools-1.9/test/setGT.samples.txt]="het" & binom(AD[@/build/bcftools-1.9/test/setGT.samples.txt])<0.1' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/setGT.2.bcf -- -t q -n . -i 'GT[@/build/bcftools-1.9/test/setGT.samples.txt]="het" & binom(AD[@/build/bcftools-1.9/test/setGT.samples.txt])<0.1' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-1.9/test/annotate9.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-1.9/test/annotate9.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-AN-AC --no-version /tmp/RsCoEawrJC/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-AN-AC --no-version /tmp/RsCoEawrJC/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +dosage /tmp/RsCoEawrJC/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +dosage /tmp/RsCoEawrJC/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixploidy --no-version /tmp/RsCoEawrJC/fixploidy.vcf.gz -- -s /build/bcftools-1.9/test/fixploidy.samples -p /build/bcftools-1.9/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixploidy --no-version /tmp/RsCoEawrJC/fixploidy.bcf -- -s /build/bcftools-1.9/test/fixploidy.samples -p /build/bcftools-1.9/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +guess-ploidy /tmp/RsCoEawrJC/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +guess-ploidy /tmp/RsCoEawrJC/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +guess-ploidy /tmp/RsCoEawrJC/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ Warning: PL tag not found in header, switching to GL .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +guess-ploidy /tmp/RsCoEawrJC/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ Warning: PL tag not found in header, switching to GL .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +tag2tag --no-version /tmp/RsCoEawrJC/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +tag2tag --no-version /tmp/RsCoEawrJC/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +tag2tag --no-version /tmp/RsCoEawrJC/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +tag2tag --no-version /tmp/RsCoEawrJC/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/view.vcf.gz -- -t AC -S /build/bcftools-1.9/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/view.bcf -- -t AC -S /build/bcftools-1.9/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +trio-switch-rate /tmp/RsCoEawrJC/trio.vcf.gz -- -p /build/bcftools-1.9/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +trio-switch-rate /tmp/RsCoEawrJC/trio.bcf -- -p /build/bcftools-1.9/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +trio-stats /tmp/RsCoEawrJC/trio-stats.vcf.gz -p /build/bcftools-1.9/test/trio-stats.ped | grep -v ^CMD 2>/dev/null | grep -v ^##bcftools_ Identified 2 complete trios in the VCF file .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +trio-stats /tmp/RsCoEawrJC/trio-stats.bcf -p /build/bcftools-1.9/test/trio-stats.ped | grep -v ^CMD 2>/dev/null | grep -v ^##bcftools_ Identified 2 complete trios in the VCF file .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +ad-bias /tmp/RsCoEawrJC/ad-bias.vcf.gz -- -s /build/bcftools-1.9/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +ad-bias /tmp/RsCoEawrJC/ad-bias.bcf -- -s /build/bcftools-1.9/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +af-dist /tmp/RsCoEawrJC/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +af-dist /tmp/RsCoEawrJC/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixref /tmp/RsCoEawrJC/fixref.2a.vcf.gz -- -f /build/bcftools-1.9/test/norm.fa -i /tmp/RsCoEawrJC/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixref /tmp/RsCoEawrJC/fixref.2a.bcf -- -f /build/bcftools-1.9/test/norm.fa -i /tmp/RsCoEawrJC/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixref /tmp/RsCoEawrJC/fixref.3.vcf.gz -- -f /build/bcftools-1.9/test/fixref.3.fa -m top 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixref /tmp/RsCoEawrJC/fixref.3.bcf -- -f /build/bcftools-1.9/test/fixref.3.fa -m top 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-from-fasta /tmp/RsCoEawrJC/aa.vcf.gz -- -f /build/bcftools-1.9/test/aa.fa -c AA -h /build/bcftools-1.9/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-from-fasta /tmp/RsCoEawrJC/aa.bcf -- -f /build/bcftools-1.9/test/aa.fa -c AA -h /build/bcftools-1.9/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-from-fasta /tmp/RsCoEawrJC/ref.vcf.gz -- -f /build/bcftools-1.9/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-from-fasta /tmp/RsCoEawrJC/ref.bcf -- -f /build/bcftools-1.9/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/RsCoEawrJC/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/RsCoEawrJC/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/RsCoEawrJC/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/RsCoEawrJC/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/RsCoEawrJC/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/RsCoEawrJC/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +mendelian /tmp/RsCoEawrJC/mendelian.vcf.gz -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +mendelian /tmp/RsCoEawrJC/mendelian.bcf -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +mendelian /tmp/RsCoEawrJC/mendelian.vcf.gz -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +mendelian /tmp/RsCoEawrJC/mendelian.bcf -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +mendelian /tmp/RsCoEawrJC/mendelian.vcf.gz -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +mendelian /tmp/RsCoEawrJC/mendelian.bcf -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +contrast /tmp/RsCoEawrJC/contrast.vcf.gz -0 a,b -1 c 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +contrast /tmp/RsCoEawrJC/contrast.bcf -0 a,b -1 c 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat --no-version /tmp/RsCoEawrJC/concat.1.a.vcf.gz /tmp/RsCoEawrJC/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob /tmp/RsCoEawrJC/concat.1.a.vcf.gz /tmp/RsCoEawrJC/concat.1.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat --no-version /tmp/RsCoEawrJC/concat.1.a.bcf /tmp/RsCoEawrJC/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob /tmp/RsCoEawrJC/concat.1.a.bcf /tmp/RsCoEawrJC/concat.1.b.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat --no-version -a /tmp/RsCoEawrJC/concat.2.a.vcf.gz /tmp/RsCoEawrJC/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -a /tmp/RsCoEawrJC/concat.2.a.vcf.gz /tmp/RsCoEawrJC/concat.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat --no-version -a /tmp/RsCoEawrJC/concat.2.a.bcf /tmp/RsCoEawrJC/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -a /tmp/RsCoEawrJC/concat.2.a.bcf /tmp/RsCoEawrJC/concat.2.b.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat --no-version -aD /tmp/RsCoEawrJC/concat.2.a.vcf.gz /tmp/RsCoEawrJC/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -aD /tmp/RsCoEawrJC/concat.2.a.vcf.gz /tmp/RsCoEawrJC/concat.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat --no-version -aD /tmp/RsCoEawrJC/concat.2.a.bcf /tmp/RsCoEawrJC/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -aD /tmp/RsCoEawrJC/concat.2.a.bcf /tmp/RsCoEawrJC/concat.2.b.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat --no-version -l /tmp/RsCoEawrJC/concat.3.a.vcf.gz /tmp/RsCoEawrJC/concat.3.b.vcf.gz /tmp/RsCoEawrJC/concat.3.0.vcf.gz /tmp/RsCoEawrJC/concat.3.c.vcf.gz /tmp/RsCoEawrJC/concat.3.d.vcf.gz /tmp/RsCoEawrJC/concat.3.e.vcf.gz /tmp/RsCoEawrJC/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -l /tmp/RsCoEawrJC/concat.3.a.vcf.gz /tmp/RsCoEawrJC/concat.3.b.vcf.gz /tmp/RsCoEawrJC/concat.3.0.vcf.gz /tmp/RsCoEawrJC/concat.3.c.vcf.gz /tmp/RsCoEawrJC/concat.3.d.vcf.gz /tmp/RsCoEawrJC/concat.3.e.vcf.gz /tmp/RsCoEawrJC/concat.3.f.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat --no-version -l /tmp/RsCoEawrJC/concat.3.a.bcf /tmp/RsCoEawrJC/concat.3.b.bcf /tmp/RsCoEawrJC/concat.3.0.bcf /tmp/RsCoEawrJC/concat.3.c.bcf /tmp/RsCoEawrJC/concat.3.d.bcf /tmp/RsCoEawrJC/concat.3.e.bcf /tmp/RsCoEawrJC/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -l /tmp/RsCoEawrJC/concat.3.a.bcf /tmp/RsCoEawrJC/concat.3.b.bcf /tmp/RsCoEawrJC/concat.3.0.bcf /tmp/RsCoEawrJC/concat.3.c.bcf /tmp/RsCoEawrJC/concat.3.d.bcf /tmp/RsCoEawrJC/concat.3.e.bcf /tmp/RsCoEawrJC/concat.3.f.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 2002330770 .. ok test_naive_concat: /build/bcftools-1.9/bcftools concat --naive /tmp/RsCoEawrJC/naive_concat.0.bcf /tmp/RsCoEawrJC/naive_concat.1.bcf /tmp/RsCoEawrJC/naive_concat.2.bcf /tmp/RsCoEawrJC/naive_concat.3.bcf /tmp/RsCoEawrJC/naive_concat.4.bcf /tmp/RsCoEawrJC/naive_concat.5.bcf /tmp/RsCoEawrJC/naive_concat.6.bcf /tmp/RsCoEawrJC/naive_concat.7.bcf /tmp/RsCoEawrJC/naive_concat.8.bcf /tmp/RsCoEawrJC/naive_concat.9.bcf | /build/bcftools-1.9/bcftools view -H .. ok test_naive_concat: /build/bcftools-1.9/bcftools concat --naive /tmp/RsCoEawrJC/naive_concat.0.vcf.gz /tmp/RsCoEawrJC/naive_concat.1.vcf.gz /tmp/RsCoEawrJC/naive_concat.2.vcf.gz /tmp/RsCoEawrJC/naive_concat.3.vcf.gz /tmp/RsCoEawrJC/naive_concat.4.vcf.gz /tmp/RsCoEawrJC/naive_concat.5.vcf.gz /tmp/RsCoEawrJC/naive_concat.6.vcf.gz /tmp/RsCoEawrJC/naive_concat.7.vcf.gz /tmp/RsCoEawrJC/naive_concat.8.vcf.gz /tmp/RsCoEawrJC/naive_concat.9.vcf.gz | /build/bcftools-1.9/bcftools view -H .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr /build/bcftools-1.9/test/empty.vcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.9/test/empty.vcf | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr /tmp/RsCoEawrJC/empty.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/RsCoEawrJC/empty.bcf | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr /tmp/RsCoEawrJC/empty.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/RsCoEawrJC/empty.vcf.gz | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr | /build/bcftools-1.9/bcftools view --no-version .. ok test_rename_chrs: /build/bcftools-1.9/bcftools annotate --rename-chrs /tmp/RsCoEawrJC/rename.map -Ov /tmp/RsCoEawrJC/annotate.bcf | /build/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.9/bcftools annotate --rename-chrs /tmp/RsCoEawrJC/rename.map -Ob /tmp/RsCoEawrJC/annotate.bcf | /build/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.9/bcftools annotate --rename-chrs /tmp/RsCoEawrJC/rename.map -Ov /build/bcftools-1.9/test/annotate.vcf | /build/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.9/bcftools annotate --rename-chrs /tmp/RsCoEawrJC/rename.map -Ob /build/bcftools-1.9/test/annotate.vcf | /build/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert -g -,. /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert -g .,- /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert -g -,. --tag PL /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. --tag PL 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert -g .,- --tag PL /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- --tag PL 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert -g -,. --vcf-ids /tmp/RsCoEawrJC/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. --vcf-ids 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert -g .,- --vcf-ids /tmp/RsCoEawrJC/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- --vcf-ids 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert -g -,. --chrom /tmp/RsCoEawrJC/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. --chrom 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert -g .,- --chrom /tmp/RsCoEawrJC/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- --chrom 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert -g -,. --chrom --vcf-ids /tmp/RsCoEawrJC/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert -g .,- --chrom --vcf-ids /tmp/RsCoEawrJC/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert -h -,.,. /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -h -,.,. 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert -h .,-,. /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -h .,-,. 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert -h .,.,- /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -h .,.,- 2>/dev/null .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.9/bcftools convert -H /build/bcftools-1.9/test/convert.hls.gt.hap,/build/bcftools-1.9/test/convert.hls.gt.legend,/build/bcftools-1.9/test/convert.hls.gt.samples 2>/dev/null | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.9/bcftools convert -H /build/bcftools-1.9/test/convert.hls.gt.hap,/build/bcftools-1.9/test/convert.hls.gt.legend,/build/bcftools-1.9/test/convert.hls.gt.samples -Ou 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.9/bcftools convert --hapsample2vcf /build/bcftools-1.9/test/convert.hs.gt.hap,/build/bcftools-1.9/test/convert.hs.gt.samples 2>/dev/null | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.9/bcftools convert --hapsample2vcf /build/bcftools-1.9/test/convert.hs.gt.hap,/build/bcftools-1.9/test/convert.hs.gt.samples -Ou 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert --hapsample -,. /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert --hapsample -,. 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert --hapsample .,- /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert --hapsample .,- 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert --haplegendsample -,.,. /tmp/RsCoEawrJC/convert.hap-missing.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.hap-missing.vcf.gz | /build/bcftools-1.9/bcftools convert --haplegendsample -,.,. 2>/dev/null .. ok test_vcf_convert_gvcf: /build/bcftools-1.9/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.9/test/gvcf.fa /tmp/RsCoEawrJC/convert.gvcf.vcf.gz 2>/dev/null .. ok test_vcf_convert_gvcf: /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.gvcf.vcf.gz | /build/bcftools-1.9/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.9/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/bcftools-1.9/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-1.9/test/23andme.fa --tsv2vcf /build/bcftools-1.9/test/convert.23andme 2>/dev/null .. ok test_vcf_convert_tsv2vcf: /build/bcftools-1.9/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-1.9/test/23andme.fa --tsv2vcf /build/bcftools-1.9/test/convert.23andme 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -m /build/bcftools-1.9/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -m /build/bcftools-1.9/test/consensus.tab -c /tmp/RsCoEawrJC/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/RsCoEawrJC/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 -m /build/bcftools-1.9/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 -m /build/bcftools-1.9/test/consensus.tab -c /tmp/RsCoEawrJC/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/RsCoEawrJC/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -I -m /build/bcftools-1.9/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -I -m /build/bcftools-1.9/test/consensus.tab -c /tmp/RsCoEawrJC/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/RsCoEawrJC/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 2>/dev/null .. ok test_vcf_consensus_chain: /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 -c /tmp/RsCoEawrJC/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/RsCoEawrJC/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus2.vcf.gz -f /build/bcftools-1.9/test/consensus2.fa -H 1 2>/dev/null .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus2.vcf.gz -f /build/bcftools-1.9/test/consensus2.fa -H 2 2>/dev/null .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/empty.vcf.gz -f /build/bcftools-1.9/test/consensus.fa 2>/dev/null .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus3.vcf.gz -f /build/bcftools-1.9/test/consensus2.fa -H 2 -M "?" 2>/dev/null .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -b /tmp/RsCoEawrJC/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob -b /tmp/RsCoEawrJC/mpileup.bam.urllist 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -b /tmp/RsCoEawrJC/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob -b /tmp/RsCoEawrJC/mpileup.cram.urllist 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/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 /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/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 /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/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 /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/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 /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S /build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S /build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S /build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S /build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -S /build/bcftools-1.9/test/mplp.9.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -S /build/bcftools-1.9/test/mplp.9.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -S /build/bcftools-1.9/test/mplp.9.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -S /build/bcftools-1.9/test/mplp.9.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -G /build/bcftools-1.9/test/mplp.10.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -G /build/bcftools-1.9/test/mplp.10.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -G /build/bcftools-1.9/test/mplp.10.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -G /build/bcftools-1.9/test/mplp.10.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a AD -f /build/bcftools-1.9/test/mpileup/indel-AD.1.fa /build/bcftools-1.9/test/mpileup/indel-AD.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a AD -f /build/bcftools-1.9/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.9/test/mpileup/indel-AD.1.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a AD -f /build/bcftools-1.9/test/mpileup/indel-AD.1.fa /build/bcftools-1.9/test/mpileup/indel-AD.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a AD -f /build/bcftools-1.9/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.9/test/mpileup/indel-AD.1.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq.fa -g /build/bcftools-1.9/test/csq.gff3 /build/bcftools-1.9/test/csq.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq.gff3 ... Indexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000528237/ENST00000528237.fa -g /build/bcftools-1.9/test/csq/ENST00000528237/ENST00000528237.gff /build/bcftools-1.9/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000528237/ENST00000528237.gff ... Indexed 1 transcripts, 7 exons, 6 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000448695/ENST00000448695.fa -g /build/bcftools-1.9/test/csq/ENST00000448695/ENST00000448695.gff /build/bcftools-1.9/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000448695/ENST00000448695.gff ... Indexed 1 transcripts, 26 exons, 26 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000413103/ENST00000413103.fa -g /build/bcftools-1.9/test/csq/ENST00000413103/ENST00000413103.gff /build/bcftools-1.9/test/csq/ENST00000413103/long-deletion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000413103/ENST00000413103.gff ... Indexed 1 transcripts, 2 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.9/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.9/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000256452/ENST00000256452.fa -g /build/bcftools-1.9/test/csq/ENST00000256452/ENST00000256452.gff /build/bcftools-1.9/test/csq/ENST00000256452/intron.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000256452/ENST00000256452.gff ... Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000409523/ENST00000409523.fa -g /build/bcftools-1.9/test/csq/ENST00000409523/ENST00000409523.gff /build/bcftools-1.9/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000409523/ENST00000409523.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000593942/ENST00000593942.fa -g /build/bcftools-1.9/test/csq/ENST00000593942/ENST00000593942.gff /build/bcftools-1.9/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000593942/ENST00000593942.gff ... Indexed 1 transcripts, 7 exons, 4 CDSs, 5 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000519442/ENST00000519442.fa -g /build/bcftools-1.9/test/csq/ENST00000519442/ENST00000519442.gff /build/bcftools-1.9/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000519442/ENST00000519442.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.9/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.9/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000520868/ENST00000520868.fa -g /build/bcftools-1.9/test/csq/ENST00000520868/ENST00000520868.gff /build/bcftools-1.9/test/csq/ENST00000520868/long-deletion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000520868/ENST00000520868.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.9/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.9/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.9/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.gff ... Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.9/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.gff ... Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.9/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.gff ... Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.9/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.gff ... Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/bcftools-1.9/test/csq/ENSG00000173376/ENSG00000173376.gff /build/bcftools-1.9/test/csq/ENSG00000173376/synon.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENSG00000173376/ENSG00000173376.gff ... Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-1.9/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-1.9/test/csq/ENST00000420670/start-stop-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000420670/ENST00000420670.gff ... Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000375992/ENST00000375992.fa -g /build/bcftools-1.9/test/csq/ENST00000375992/ENST00000375992.gff /build/bcftools-1.9/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000375992/ENST00000375992.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.9/test/csq/ENST00000218032/start-lost-del.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.9/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.9/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000545279/ENST00000545279.fa -g /build/bcftools-1.9/test/csq/ENST00000545279/ENST00000545279.gff /build/bcftools-1.9/test/csq/ENST00000545279/splice-region-insert.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000545279/ENST00000545279.gff ... Indexed 1 transcripts, 9 exons, 7 CDSs, 4 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000436063/ENST00000436063.fa -g /build/bcftools-1.9/test/csq/ENST00000436063/ENST00000436063.gff /build/bcftools-1.9/test/csq/ENST00000436063/insert-before-utr.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000436063/ENST00000436063.gff ... Indexed 1 transcripts, 7 exons, 7 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000271583/ENST00000271583.fa -g /build/bcftools-1.9/test/csq/ENST00000271583/ENST00000271583.gff /build/bcftools-1.9/test/csq/ENST00000271583/splice-acceptor.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000271583/ENST00000271583.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.9/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.9/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.9/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.9/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.9/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.9/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000357367/ENST00000357367.fa -g /build/bcftools-1.9/test/csq/ENST00000357367/ENST00000357367.gff /build/bcftools-1.9/test/csq/ENST00000357367/stop-retained.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000357367/ENST00000357367.gff ... Indexed 1 transcripts, 4 exons, 3 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.9/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.gff ... Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.9/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.gff ... Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000382647/ENST00000382647.fa -g /build/bcftools-1.9/test/csq/ENST00000382647/ENST00000382647.gff /build/bcftools-1.9/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000382647/ENST00000382647.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000624631/ENST00000624631.fa -g /build/bcftools-1.9/test/csq/ENST00000624631/ENST00000624631.gff /build/bcftools-1.9/test/csq/ENST00000624631/ambiguous.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000624631/ENST00000624631.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000301246/ENST00000301246.fa -g /build/bcftools-1.9/test/csq/ENST00000301246/ENST00000301246.gff /build/bcftools-1.9/test/csq/ENST00000301246/15bp-insert.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000301246/ENST00000301246.gff ... Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000557788/ENST00000557788.fa -g /build/bcftools-1.9/test/csq/ENST00000557788/ENST00000557788.gff /build/bcftools-1.9/test/csq/ENST00000557788/long-overlap-del.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000557788/ENST00000557788.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000227471/ENST00000227471.fa -g /build/bcftools-1.9/test/csq/ENST00000227471/ENST00000227471.gff /build/bcftools-1.9/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000227471/ENST00000227471.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000410009/ENST00000410009.fa -g /build/bcftools-1.9/test/csq/ENST00000410009/ENST00000410009.gff /build/bcftools-1.9/test/csq/ENST00000410009/frameshift.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000410009/ENST00000410009.gff ... Indexed 1 transcripts, 6 exons, 6 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.9/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.9/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.9/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.9/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.9/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.9/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.9/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.gff ... Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.9/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.gff ... Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.9/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.gff ... Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.9/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.gff ... Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000390520/ENST00000390520.fa -g /build/bcftools-1.9/test/csq/ENST00000390520/ENST00000390520.gff /build/bcftools-1.9/test/csq/ENST00000390520/deletion-overlap.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000390520/ENST00000390520.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000368801/ENST00000368801.fa -g /build/bcftools-1.9/test/csq/ENST00000368801/ENST00000368801.gff /build/bcftools-1.9/test/csq/ENST00000368801/compound-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000368801/ENST00000368801.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000381157/ENST00000381157.fa -g /build/bcftools-1.9/test/csq/ENST00000381157/ENST00000381157.gff /build/bcftools-1.9/test/csq/ENST00000381157/haploid-diploid.vcf | /build/bcftools-1.9/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' Parsing /build/bcftools-1.9/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: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.9/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.gff ... Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.9/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.gff ... Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs Calling... .. ok Number of tests: total .. 821 passed .. 821 failed .. 0 make[1]: Leaving directory '/build/bcftools-1.9' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j4 install DESTDIR=/build/bcftools-1.9/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/bcftools-1.9' mkdir -p -m 755 /build/bcftools-1.9/debian/bcftools/usr/bin /build/bcftools-1.9/debian/bcftools/usr/share/man/man1 /build/bcftools-1.9/debian/bcftools/usr/lib/arm-linux-gnueabihf/bcftools install -p bcftools /build/bcftools-1.9/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /build/bcftools-1.9/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/bcftools-1.9/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/bcftools-1.9/debian/bcftools/usr/lib/arm-linux-gnueabihf/bcftools make[1]: Leaving directory '/build/bcftools-1.9' debian/rules override_dh_install make[1]: Entering directory '/build/bcftools-1.9' dh_install # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/build/bcftools-1.9' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/bcftools-1.9' dh_installman --language=C make[1]: Leaving directory '/build/bcftools-1.9' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools' in '../bcftools_1.9-1_armhf.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.9-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bcftools_1.9-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/14432/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/14432/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/14432 and its subdirectories I: Current time: Sat Jul 18 13:41:47 +14 2020 I: pbuilder-time-stamp: 1595029307