I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 2 01:35:18 +14 2023 I: pbuilder-time-stamp: 1672572918 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/1050109/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. 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/1050109/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1050109/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]="x86_64-pc-linux-gnu") 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=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=6ba712b8bc2a4aae92e28736c539ebbe LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu 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=1050109 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.cDBzYlCgoz/pbuilderrc_xROe --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.cDBzYlCgoz/b2 --logfile b2/build.log bcftools_1.9-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 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 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 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 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 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 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 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 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 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 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jan 2 01:35 sh -> bash lrwxrwxrwx 1 root root 4 Dec 11 18:21 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 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/1050109/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: amd64 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 ... 19195 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 30.0 MB of archives. After unpacking 96.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libbz2-dev amd64 1.0.6-9.2~deb10u1 [30.2 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libgslcblas0 amd64 2.5+dfsg-6 [101 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libgsl23 amd64 2.5+dfsg-6 [880 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libgsl-dev amd64 2.5+dfsg-6 [1063 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 liblzma-dev amd64 5.2.4-1 [210 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libhts-dev amd64 1.9-12~deb10u1 [4347 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 tabix amd64 1.9-12~deb10u1 [292 kB] Fetched 30.0 MB in 1s (59.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.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+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../11-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_amd64.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 ... 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Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libgsl23:amd64 (2.5+dfsg-6) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up liblzma-dev:amd64 (5.2.4-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up libbz2-dev:amd64 (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:amd64 (2.4.47+dfsg-3+deb10u6) ... 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:amd64 (1.17-3+deb10u3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... 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:amd64 (7.64.0-4+deb10u2) ... 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 (1.9-12~deb10u1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:amd64 (1.9-12~deb10u1) ... 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 hostname: Name or service not known 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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../bcftools_1.9-1_source.changes 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 amd64 fakeroot debian/rules clean rm -f config.mk && touch config.mk dh clean dh_auto_clean make -j16 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/x86_64-linux-gnu/bcftools ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether 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... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -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 -j16 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 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/x86_64-linux-gnu/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/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/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/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/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/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/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/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/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/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/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 -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 -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 -j16 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/t6JD9HuTKs/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-1.9/bcftools view -H /tmp/t6JD9HuTKs/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/t6JD9HuTKs/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-1.9/bcftools view -H /tmp/t6JD9HuTKs/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/t6JD9HuTKs/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/t6JD9HuTKs/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/t6JD9HuTKs/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/t6JD9HuTKs/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/t6JD9HuTKs/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/t6JD9HuTKs/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/t6JD9HuTKs/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/t6JD9HuTKs/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/t6JD9HuTKs/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/t6JD9HuTKs/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/t6JD9HuTKs/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/t6JD9HuTKs/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/t6JD9HuTKs/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/t6JD9HuTKs/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/t6JD9HuTKs/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/t6JD9HuTKs/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/t6JD9HuTKs/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/t6JD9HuTKs/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/t6JD9HuTKs/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/t6JD9HuTKs/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/t6JD9HuTKs/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/t6JD9HuTKs/empty.bcf .. ok test_vcf_check: /build/bcftools-1.9/bcftools stats -s - /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/check.1.chk /tmp/t6JD9HuTKs/check.2.chk /tmp/t6JD9HuTKs/check.3.chk /tmp/t6JD9HuTKs/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/t6JD9HuTKs/stats.a.vcf.gz /tmp/t6JD9HuTKs/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.9/bcftools stats -s B /tmp/t6JD9HuTKs/stats.a.vcf.gz /tmp/t6JD9HuTKs/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.9/bcftools stats -s - /tmp/t6JD9HuTKs/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -n =2 /tmp/t6JD9HuTKs/isec.a.vcf.gz /tmp/t6JD9HuTKs/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -Ob -n =2 /tmp/t6JD9HuTKs/isec.a.vcf.gz /tmp/t6JD9HuTKs/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/t6JD9HuTKs/isec.a.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/isec.a.vcf.gz /tmp/t6JD9HuTKs/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -n =2 -c both /tmp/t6JD9HuTKs/isec.a.vcf.gz /tmp/t6JD9HuTKs/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -Ob -n =2 -c both /tmp/t6JD9HuTKs/isec.a.vcf.gz /tmp/t6JD9HuTKs/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -n =2 -c any /tmp/t6JD9HuTKs/isec.a.vcf.gz /tmp/t6JD9HuTKs/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -Ob -n =2 -c any /tmp/t6JD9HuTKs/isec.a.vcf.gz /tmp/t6JD9HuTKs/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -C -c any /tmp/t6JD9HuTKs/isec.a.vcf.gz /tmp/t6JD9HuTKs/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -Ob -C -c any /tmp/t6JD9HuTKs/isec.a.vcf.gz /tmp/t6JD9HuTKs/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /build/bcftools-1.9/bcftools isec --no-version -T /tmp/t6JD9HuTKs/isec.tab.gz /tmp/t6JD9HuTKs/isec.a.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /build/bcftools-1.9/bcftools isec -Ob -T /tmp/t6JD9HuTKs/isec.tab.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/merge.a.vcf.gz /tmp/t6JD9HuTKs/merge.b.vcf.gz /tmp/t6JD9HuTKs/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples /tmp/t6JD9HuTKs/merge.a.vcf.gz /tmp/t6JD9HuTKs/merge.b.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/merge.a.vcf.gz /tmp/t6JD9HuTKs/merge.b.vcf.gz /tmp/t6JD9HuTKs/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -Fx /tmp/t6JD9HuTKs/merge.a.vcf.gz /tmp/t6JD9HuTKs/merge.b.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/merge.a.vcf.gz /tmp/t6JD9HuTKs/merge.b.vcf.gz /tmp/t6JD9HuTKs/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -0 /tmp/t6JD9HuTKs/merge.a.vcf.gz /tmp/t6JD9HuTKs/merge.b.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/merge.2.a.vcf.gz /tmp/t6JD9HuTKs/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -m none /tmp/t6JD9HuTKs/merge.2.a.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/merge.2.a.vcf.gz /tmp/t6JD9HuTKs/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -m both /tmp/t6JD9HuTKs/merge.2.a.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/merge.2.a.vcf.gz /tmp/t6JD9HuTKs/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -m all /tmp/t6JD9HuTKs/merge.2.a.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/merge.3.a.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/merge.3.a.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/merge.4.a.vcf.gz /tmp/t6JD9HuTKs/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -m id /tmp/t6JD9HuTKs/merge.4.a.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/gvcf.merge.1.vcf.gz /tmp/t6JD9HuTKs/gvcf.merge.2.vcf.gz /tmp/t6JD9HuTKs/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/t6JD9HuTKs/gvcf.merge.1.vcf.gz /tmp/t6JD9HuTKs/gvcf.merge.2.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/merge.gvcf.2.a.vcf.gz /tmp/t6JD9HuTKs/merge.gvcf.2.b.vcf.gz /tmp/t6JD9HuTKs/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/t6JD9HuTKs/merge.gvcf.2.a.vcf.gz /tmp/t6JD9HuTKs/merge.gvcf.2.b.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/merge.gvcf.3.a.vcf.gz /tmp/t6JD9HuTKs/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --gvcf - -i SRC:join /tmp/t6JD9HuTKs/merge.gvcf.3.a.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/merge.5.a.vcf.gz /tmp/t6JD9HuTKs/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob /tmp/t6JD9HuTKs/merge.5.a.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m- /tmp/t6JD9HuTKs/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/t6JD9HuTKs/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m- /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/t6JD9HuTKs/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/t6JD9HuTKs/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/t6JD9HuTKs/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/t6JD9HuTKs/norm.merge.3.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/t6JD9HuTKs/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/t6JD9HuTKs/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m+ -s /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d snps /tmp/t6JD9HuTKs/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/t6JD9HuTKs/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d indels /tmp/t6JD9HuTKs/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/t6JD9HuTKs/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d both /tmp/t6JD9HuTKs/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/t6JD9HuTKs/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d all /tmp/t6JD9HuTKs/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/t6JD9HuTKs/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d none /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -f PASS -Xks NA00003 /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -xs NA00003 /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -p /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -P /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -GVsnps /tmp/t6JD9HuTKs/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -GVsnps /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -s ^NA00003 /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -G /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -a /tmp/t6JD9HuTKs/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -a /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -asA /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -asB /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -asA /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/t6JD9HuTKs/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i'TXT0="text"' /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -i 'POS>=3062917' /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -c6:nonmajor /tmp/t6JD9HuTKs/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -q0.3:major /tmp/t6JD9HuTKs/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/t6JD9HuTKs/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/t6JD9HuTKs/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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.BiTCIY 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.QVMaK1 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.Moab03 Merging 5 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.ZeFJ66 Merging 5 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/t6JD9HuTKs/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/t6JD9HuTKs/regions.tab.gz /tmp/t6JD9HuTKs/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/t6JD9HuTKs/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/t6JD9HuTKs/regions.tab.gz /tmp/t6JD9HuTKs/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/t6JD9HuTKs/regions.bed /tmp/t6JD9HuTKs/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/t6JD9HuTKs/regions.bed .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/t6JD9HuTKs/regions.bed /tmp/t6JD9HuTKs/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/t6JD9HuTKs/regions.bed.gz /tmp/t6JD9HuTKs/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/t6JD9HuTKs/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/t6JD9HuTKs/regions.bed.gz /tmp/t6JD9HuTKs/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots4.vcf.gz -c +INFO /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots4.vcf.gz -c +INFO /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots11.vcf.gz -c FMT /tmp/t6JD9HuTKs/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/t6JD9HuTKs/annots11.vcf.gz -c FMT /tmp/t6JD9HuTKs/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/t6JD9HuTKs/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +missing2ref --no-version /tmp/t6JD9HuTKs/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +setGT --no-version /tmp/t6JD9HuTKs/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/t6JD9HuTKs/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +setGT --no-version /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-AN-AC --no-version /tmp/t6JD9HuTKs/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +dosage /tmp/t6JD9HuTKs/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +dosage /tmp/t6JD9HuTKs/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixploidy --no-version /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/t6JD9HuTKs/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/t6JD9HuTKs/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixref /tmp/t6JD9HuTKs/fixref.2a.vcf.gz -- -f /build/bcftools-1.9/test/norm.fa -i /tmp/t6JD9HuTKs/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixref /tmp/t6JD9HuTKs/fixref.2a.bcf -- -f /build/bcftools-1.9/test/norm.fa -i /tmp/t6JD9HuTKs/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixref /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/t6JD9HuTKs/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/t6JD9HuTKs/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/t6JD9HuTKs/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +mendelian /tmp/t6JD9HuTKs/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/t6JD9HuTKs/mendelian.bcf -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +mendelian /tmp/t6JD9HuTKs/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/t6JD9HuTKs/mendelian.bcf -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +mendelian /tmp/t6JD9HuTKs/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/t6JD9HuTKs/mendelian.bcf -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +contrast /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/concat.1.a.vcf.gz /tmp/t6JD9HuTKs/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob /tmp/t6JD9HuTKs/concat.1.a.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/concat.1.a.bcf /tmp/t6JD9HuTKs/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob /tmp/t6JD9HuTKs/concat.1.a.bcf /tmp/t6JD9HuTKs/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/t6JD9HuTKs/concat.2.a.vcf.gz /tmp/t6JD9HuTKs/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -a /tmp/t6JD9HuTKs/concat.2.a.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/concat.2.a.bcf /tmp/t6JD9HuTKs/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -a /tmp/t6JD9HuTKs/concat.2.a.bcf /tmp/t6JD9HuTKs/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/t6JD9HuTKs/concat.2.a.vcf.gz /tmp/t6JD9HuTKs/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -aD /tmp/t6JD9HuTKs/concat.2.a.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/concat.2.a.bcf /tmp/t6JD9HuTKs/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -aD /tmp/t6JD9HuTKs/concat.2.a.bcf /tmp/t6JD9HuTKs/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/t6JD9HuTKs/concat.3.a.vcf.gz /tmp/t6JD9HuTKs/concat.3.b.vcf.gz /tmp/t6JD9HuTKs/concat.3.0.vcf.gz /tmp/t6JD9HuTKs/concat.3.c.vcf.gz /tmp/t6JD9HuTKs/concat.3.d.vcf.gz /tmp/t6JD9HuTKs/concat.3.e.vcf.gz /tmp/t6JD9HuTKs/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -l /tmp/t6JD9HuTKs/concat.3.a.vcf.gz /tmp/t6JD9HuTKs/concat.3.b.vcf.gz /tmp/t6JD9HuTKs/concat.3.0.vcf.gz /tmp/t6JD9HuTKs/concat.3.c.vcf.gz /tmp/t6JD9HuTKs/concat.3.d.vcf.gz /tmp/t6JD9HuTKs/concat.3.e.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/concat.3.a.bcf /tmp/t6JD9HuTKs/concat.3.b.bcf /tmp/t6JD9HuTKs/concat.3.0.bcf /tmp/t6JD9HuTKs/concat.3.c.bcf /tmp/t6JD9HuTKs/concat.3.d.bcf /tmp/t6JD9HuTKs/concat.3.e.bcf /tmp/t6JD9HuTKs/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -l /tmp/t6JD9HuTKs/concat.3.a.bcf /tmp/t6JD9HuTKs/concat.3.b.bcf /tmp/t6JD9HuTKs/concat.3.0.bcf /tmp/t6JD9HuTKs/concat.3.c.bcf /tmp/t6JD9HuTKs/concat.3.d.bcf /tmp/t6JD9HuTKs/concat.3.e.bcf /tmp/t6JD9HuTKs/concat.3.f.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 3225494553 .. ok test_naive_concat: /build/bcftools-1.9/bcftools concat --naive /tmp/t6JD9HuTKs/naive_concat.0.bcf /tmp/t6JD9HuTKs/naive_concat.1.bcf /tmp/t6JD9HuTKs/naive_concat.2.bcf /tmp/t6JD9HuTKs/naive_concat.3.bcf /tmp/t6JD9HuTKs/naive_concat.4.bcf /tmp/t6JD9HuTKs/naive_concat.5.bcf /tmp/t6JD9HuTKs/naive_concat.6.bcf /tmp/t6JD9HuTKs/naive_concat.7.bcf /tmp/t6JD9HuTKs/naive_concat.8.bcf /tmp/t6JD9HuTKs/naive_concat.9.bcf | /build/bcftools-1.9/bcftools view -H .. ok test_naive_concat: /build/bcftools-1.9/bcftools concat --naive /tmp/t6JD9HuTKs/naive_concat.0.vcf.gz /tmp/t6JD9HuTKs/naive_concat.1.vcf.gz /tmp/t6JD9HuTKs/naive_concat.2.vcf.gz /tmp/t6JD9HuTKs/naive_concat.3.vcf.gz /tmp/t6JD9HuTKs/naive_concat.4.vcf.gz /tmp/t6JD9HuTKs/naive_concat.5.vcf.gz /tmp/t6JD9HuTKs/naive_concat.6.vcf.gz /tmp/t6JD9HuTKs/naive_concat.7.vcf.gz /tmp/t6JD9HuTKs/naive_concat.8.vcf.gz /tmp/t6JD9HuTKs/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/t6JD9HuTKs/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/t6JD9HuTKs/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/t6JD9HuTKs/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/t6JD9HuTKs/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/t6JD9HuTKs/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/t6JD9HuTKs/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/t6JD9HuTKs/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/t6JD9HuTKs/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/t6JD9HuTKs/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/t6JD9HuTKs/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/t6JD9HuTKs/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/t6JD9HuTKs/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/t6JD9HuTKs/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/t6JD9HuTKs/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/t6JD9HuTKs/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/t6JD9HuTKs/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/t6JD9HuTKs/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/t6JD9HuTKs/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/t6JD9HuTKs/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/t6JD9HuTKs/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/t6JD9HuTKs/empty.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/t6JD9HuTKs/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/t6JD9HuTKs/empty.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/t6JD9HuTKs/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/t6JD9HuTKs/rename.map -Ov /tmp/t6JD9HuTKs/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/t6JD9HuTKs/rename.map -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/convert.hap-missing.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/convert.gvcf.vcf.gz 2>/dev/null .. ok test_vcf_convert_gvcf: /build/bcftools-1.9/bcftools view -Ob /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -m /build/bcftools-1.9/test/consensus.tab -c /tmp/t6JD9HuTKs/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/t6JD9HuTKs/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/t6JD9HuTKs/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/t6JD9HuTKs/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 -m /build/bcftools-1.9/test/consensus.tab -c /tmp/t6JD9HuTKs/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/t6JD9HuTKs/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/t6JD9HuTKs/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/t6JD9HuTKs/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -I -m /build/bcftools-1.9/test/consensus.tab -c /tmp/t6JD9HuTKs/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/t6JD9HuTKs/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/t6JD9HuTKs/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/t6JD9HuTKs/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 -c /tmp/t6JD9HuTKs/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/t6JD9HuTKs/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/t6JD9HuTKs/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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-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/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-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-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/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/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/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/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/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/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/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 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/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/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/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/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/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/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/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/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/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 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 -j16 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/x86_64-linux-gnu/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/x86_64-linux-gnu/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_amd64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.9-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bcftools_1.9-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1050109/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1050109/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/1050109 and its subdirectories I: Current time: Mon Jan 2 01:37:29 +14 2023 I: pbuilder-time-stamp: 1672573049