Diff of the two buildlogs: -- --- b1/build.log 2020-07-17 23:29:54.145720413 +0000 +++ b2/build.log 2020-07-17 23:41:57.882026612 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jul 17 11:25:41 -12 2020 -I: pbuilder-time-stamp: 1595028341 +I: Current time: Sat Jul 18 13:30:11 +14 2020 +I: pbuilder-time-stamp: 1595028611 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Tue Sep 4 02:47:28 2018 -12 +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 @@ -30,136 +30,170 @@ 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/6149/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14432/tmp/hooks/D01_modify_environment starting +debug: Running on wbq0. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/14432/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14432/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='03bb0b98ebea4a22b6acca455cc6c543' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='6149' - PS1='# ' - PS2='> ' + INVOCATION_ID=9975ef5bd28b4242996926706fda3840 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=14432 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.n6w9MFigbR/pbuilderrc_bLP0 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.n6w9MFigbR/b1 --logfile b1/build.log bcftools_1.9-1.dsc' - SUDO_GID='114' - SUDO_UID='109' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.n6w9MFigbR/pbuilderrc_4v8R --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.n6w9MFigbR/b2 --logfile b2/build.log bcftools_1.9-1.dsc' + SUDO_GID=115 + SUDO_UID=111 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux ff2a 4.19.0-9-armmp-lpae #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) armv7l GNU/Linux + Linux i-capture-the-hostname 4.19.0-9-armmp #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) armv7l GNU/Linux I: ls -l /bin total 3328 - -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat - -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown - -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp - -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash - -rwxr-xr-x 1 root root 71648 Feb 28 2019 date - -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd - -rwxr-xr-x 1 root root 55672 Feb 28 2019 df - -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir - -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 18260 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount - -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln - -rwxr-xr-x 1 root root 34932 Jul 26 2018 login - -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls - -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 26024 Jan 9 2019 more - -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount - -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm - -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 16 20:25 sh -> dash - -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty - -rwsr-xr-x 1 root root 42472 Jan 9 2019 su - -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync - -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar - -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch - -rwxr-xr-x 1 root root 18260 Feb 28 2019 true - -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server - -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount - -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/6149/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 22432 Mar 1 2019 cat + -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown + -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp + -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash + -rwxr-xr-x 1 root root 71648 Mar 1 2019 date + -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd + -rwxr-xr-x 1 root root 55672 Mar 1 2019 df + -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir + -rwxr-xr-x 1 root root 54872 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 22364 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 18260 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 21980 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 124508 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 64232 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln + -rwxr-xr-x 1 root root 34932 Jul 27 2018 login + -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls + -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 26024 Jan 10 2019 more + -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount + -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 84284 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 22416 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm + -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 18 13:31 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 16 22:27 sh.distrib -> dash + -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty + -rwsr-xr-x 1 root root 42472 Jan 10 2019 su + -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync + -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar + -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch + -rwxr-xr-x 1 root root 18260 Mar 1 2019 true + -rwxr-xr-x 1 root root 9636 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount + -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 21980 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/14432/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -268,7 +302,7 @@ Get: 57 http://deb.debian.org/debian buster/main armhf libhts-dev armhf 1.9-11 [4289 kB] Get: 58 http://deb.debian.org/debian buster/main armhf libio-pty-perl armhf 1:1.08-1.1+b5 [32.9 kB] Get: 59 http://deb.debian.org/debian buster/main armhf tabix armhf 1.9-11 [263 kB] -Fetched 28.3 MB in 4s (6517 kB/s) +Fetched 28.3 MB in 17s (1637 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) @@ -527,7 +561,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/bcftools-1.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/bcftools-1.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.9-1 dpkg-buildpackage: info: source distribution unstable @@ -538,7 +572,7 @@ rm -f config.mk && touch config.mk dh clean dh_auto_clean - make -j3 distclean + make -j4 distclean make[1]: Entering directory '/build/bcftools-1.9' rm -f test/*.o test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P @@ -607,7 +641,7 @@ config.status: creating config.h make[1]: Leaving directory '/build/bcftools-1.9' dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/bcftools-1.9' echo '#define BCFTOOLS_VERSION "1.9"' > version.h gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c @@ -620,6 +654,9 @@ gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c +gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c +gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c +gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c vcfmerge.c: In function 'merge_vcf': vcfmerge.c:2334:46: warning: '__builtin___snprintf_chk' output may be truncated before the last format character [-Wformat-truncation=] char buf[10]; snprintf(buf,10,"%d",i+1); @@ -631,9 +668,6 @@ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o 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 @@ -672,28 +706,28 @@ gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl -gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/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/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split.so version.c plugins/split.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c -ldl -gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/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/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/frameshifts.so version.c plugins/frameshifts.c -ldl +gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl -gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/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/af-dist.so bin.c version.c plugins/af-dist.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl -gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/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/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl -gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/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/prune.so version.c plugins/prune.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl +gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl @@ -701,7 +735,7 @@ 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 -j3 test VERBOSE=1 + make -j4 test VERBOSE=1 make[1]: Entering directory '/build/bcftools-1.9' ./test/test-rbuf Inserted 1-9 starting at offset 5: @@ -808,1144 +842,1144 @@ .. ok test_tabix: - tabix /tmp/0aIugS0D6E/merge.a.vcf.gz 2:3199812-3199812 + tabix /tmp/RsCoEawrJC/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: - /build/bcftools-1.9/bcftools view -H /tmp/0aIugS0D6E/merge.a.bcf 2:3199812-3199812 + /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: - tabix /tmp/0aIugS0D6E/merge.a.vcf.gz 1:3000151-3000151 + tabix /tmp/RsCoEawrJC/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: - /build/bcftools-1.9/bcftools view -H /tmp/0aIugS0D6E/merge.a.bcf 1:3000151-3000151 + /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/merge.a.bcf 1:3000151-3000151 .. ok test_index: - /build/bcftools-1.9/bcftools view -H /tmp/0aIugS0D6E/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 + /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: - /build/bcftools-1.9/bcftools view -H /tmp/0aIugS0D6E/large_chrom_csi_limit.bcf chr20:1-2147483647 + /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: - /build/bcftools-1.9/bcftools view -H /tmp/0aIugS0D6E/large_chrom_csi_limit.bcf chr20:1-2147483647 + /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: - /build/bcftools-1.9/bcftools view -H /tmp/0aIugS0D6E/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 + /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: - /build/bcftools-1.9/bcftools view -H /tmp/0aIugS0D6E/large_chrom_csi_limit.bcf chr20:1-2147483647 + /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: - /build/bcftools-1.9/bcftools view -H /tmp/0aIugS0D6E/large_chrom_csi_limit.vcf.gz chr20 + /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: - /build/bcftools-1.9/bcftools view -H /tmp/0aIugS0D6E/large_chrom_csi_limit.bcf chr20 + /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.bcf chr20 .. ok test_index: - /build/bcftools-1.9/bcftools view -H /tmp/0aIugS0D6E/large_chrom_csi_limit.bcf chr20 + /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.bcf chr20 .. ok test_index: - /build/bcftools-1.9/bcftools view -H /tmp/0aIugS0D6E/large_chrom_csi_limit.vcf.gz chr20 + /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: - /build/bcftools-1.9/bcftools view -H /tmp/0aIugS0D6E/large_chrom_csi_limit.bcf chr20 + /build/bcftools-1.9/bcftools view -H /tmp/RsCoEawrJC/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: - /build/bcftools-1.9/bcftools index -s /tmp/0aIugS0D6E/idx.vcf.gz + /build/bcftools-1.9/bcftools index -s /tmp/RsCoEawrJC/idx.vcf.gz .. ok test_vcf_idxstats: - /build/bcftools-1.9/bcftools index -s /tmp/0aIugS0D6E/idx.vcf.gz + /build/bcftools-1.9/bcftools index -s /tmp/RsCoEawrJC/idx.vcf.gz .. ok test_vcf_idxstats: - /build/bcftools-1.9/bcftools index -s /tmp/0aIugS0D6E/idx.bcf + /build/bcftools-1.9/bcftools index -s /tmp/RsCoEawrJC/idx.bcf .. ok test_vcf_idxstats: - /build/bcftools-1.9/bcftools index -n /tmp/0aIugS0D6E/idx.vcf.gz + /build/bcftools-1.9/bcftools index -n /tmp/RsCoEawrJC/idx.vcf.gz .. ok test_vcf_idxstats: - /build/bcftools-1.9/bcftools index -n /tmp/0aIugS0D6E/idx.vcf.gz + /build/bcftools-1.9/bcftools index -n /tmp/RsCoEawrJC/idx.vcf.gz .. ok test_vcf_idxstats: - /build/bcftools-1.9/bcftools index -n /tmp/0aIugS0D6E/idx.bcf + /build/bcftools-1.9/bcftools index -n /tmp/RsCoEawrJC/idx.bcf .. ok test_vcf_idxstats: - /build/bcftools-1.9/bcftools index -s /tmp/0aIugS0D6E/empty.vcf.gz + /build/bcftools-1.9/bcftools index -s /tmp/RsCoEawrJC/empty.vcf.gz .. ok test_vcf_idxstats: - /build/bcftools-1.9/bcftools index -s /tmp/0aIugS0D6E/empty.vcf.gz + /build/bcftools-1.9/bcftools index -s /tmp/RsCoEawrJC/empty.vcf.gz .. ok test_vcf_idxstats: - /build/bcftools-1.9/bcftools index -s /tmp/0aIugS0D6E/empty.bcf + /build/bcftools-1.9/bcftools index -s /tmp/RsCoEawrJC/empty.bcf .. ok test_vcf_idxstats: - /build/bcftools-1.9/bcftools index -n /tmp/0aIugS0D6E/empty.vcf.gz + /build/bcftools-1.9/bcftools index -n /tmp/RsCoEawrJC/empty.vcf.gz .. ok test_vcf_idxstats: - /build/bcftools-1.9/bcftools index -n /tmp/0aIugS0D6E/empty.vcf.gz + /build/bcftools-1.9/bcftools index -n /tmp/RsCoEawrJC/empty.vcf.gz .. ok test_vcf_idxstats: - /build/bcftools-1.9/bcftools index -n /tmp/0aIugS0D6E/empty.bcf + /build/bcftools-1.9/bcftools index -n /tmp/RsCoEawrJC/empty.bcf .. ok test_vcf_check: - /build/bcftools-1.9/bcftools stats -s - /tmp/0aIugS0D6E/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' + /build/bcftools-1.9/bcftools stats -s - /tmp/RsCoEawrJC/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/check.vcf.gz | /build/bcftools-1.9/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: - /build/bcftools-1.9/misc/plot-vcfstats -m /tmp/0aIugS0D6E/check.1.chk /tmp/0aIugS0D6E/check.2.chk /tmp/0aIugS0D6E/check.3.chk /tmp/0aIugS0D6E/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' + /build/bcftools-1.9/misc/plot-vcfstats -m /tmp/RsCoEawrJC/check.1.chk /tmp/RsCoEawrJC/check.2.chk /tmp/RsCoEawrJC/check.3.chk /tmp/RsCoEawrJC/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: - /build/bcftools-1.9/bcftools stats -s - /tmp/0aIugS0D6E/stats.a.vcf.gz /tmp/0aIugS0D6E/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' + /build/bcftools-1.9/bcftools stats -s - /tmp/RsCoEawrJC/stats.a.vcf.gz /tmp/RsCoEawrJC/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: - /build/bcftools-1.9/bcftools stats -s B /tmp/0aIugS0D6E/stats.a.vcf.gz /tmp/0aIugS0D6E/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' + /build/bcftools-1.9/bcftools stats -s B /tmp/RsCoEawrJC/stats.a.vcf.gz /tmp/RsCoEawrJC/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: - /build/bcftools-1.9/bcftools stats -s - /tmp/0aIugS0D6E/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' + /build/bcftools-1.9/bcftools stats -s - /tmp/RsCoEawrJC/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: - /build/bcftools-1.9/bcftools isec -n =2 /tmp/0aIugS0D6E/isec.a.vcf.gz /tmp/0aIugS0D6E/isec.b.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools isec -n =2 /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: - /build/bcftools-1.9/bcftools isec -Ob -n =2 /tmp/0aIugS0D6E/isec.a.vcf.gz /tmp/0aIugS0D6E/isec.b.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools isec -Ob -n =2 /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: - /build/bcftools-1.9/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/0aIugS0D6E/isec.a.vcf.gz /tmp/0aIugS0D6E/isec.b.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: - /build/bcftools-1.9/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/0aIugS0D6E/isec.a.vcf.gz /tmp/0aIugS0D6E/isec.b.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: - /build/bcftools-1.9/bcftools isec -n =2 -c both /tmp/0aIugS0D6E/isec.a.vcf.gz /tmp/0aIugS0D6E/isec.b.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools isec -n =2 -c both /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: - /build/bcftools-1.9/bcftools isec -Ob -n =2 -c both /tmp/0aIugS0D6E/isec.a.vcf.gz /tmp/0aIugS0D6E/isec.b.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools isec -Ob -n =2 -c both /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: - /build/bcftools-1.9/bcftools isec -n =2 -c any /tmp/0aIugS0D6E/isec.a.vcf.gz /tmp/0aIugS0D6E/isec.b.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools isec -n =2 -c any /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: - /build/bcftools-1.9/bcftools isec -Ob -n =2 -c any /tmp/0aIugS0D6E/isec.a.vcf.gz /tmp/0aIugS0D6E/isec.b.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools isec -Ob -n =2 -c any /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: - /build/bcftools-1.9/bcftools isec -C -c any /tmp/0aIugS0D6E/isec.a.vcf.gz /tmp/0aIugS0D6E/isec.b.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools isec -C -c any /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: - /build/bcftools-1.9/bcftools isec -Ob -C -c any /tmp/0aIugS0D6E/isec.a.vcf.gz /tmp/0aIugS0D6E/isec.b.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools isec -Ob -C -c any /tmp/RsCoEawrJC/isec.a.vcf.gz /tmp/RsCoEawrJC/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: - /build/bcftools-1.9/bcftools isec --no-version -T /tmp/0aIugS0D6E/isec.tab.gz /tmp/0aIugS0D6E/isec.a.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools isec --no-version -T /tmp/RsCoEawrJC/isec.tab.gz /tmp/RsCoEawrJC/isec.a.vcf.gz 2>/dev/null .. ok test_vcf_isec2: - /build/bcftools-1.9/bcftools isec -Ob -T /tmp/0aIugS0D6E/isec.tab.gz /tmp/0aIugS0D6E/isec.a.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools isec -Ob -T /tmp/RsCoEawrJC/isec.tab.gz /tmp/RsCoEawrJC/isec.a.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge --no-version --force-samples /tmp/0aIugS0D6E/merge.a.vcf.gz /tmp/0aIugS0D6E/merge.b.vcf.gz /tmp/0aIugS0D6E/merge.c.vcf.gz + /build/bcftools-1.9/bcftools merge --no-version --force-samples /tmp/RsCoEawrJC/merge.a.vcf.gz /tmp/RsCoEawrJC/merge.b.vcf.gz /tmp/RsCoEawrJC/merge.c.vcf.gz .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge -Ob --force-samples /tmp/0aIugS0D6E/merge.a.vcf.gz /tmp/0aIugS0D6E/merge.b.vcf.gz /tmp/0aIugS0D6E/merge.c.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools merge -Ob --force-samples /tmp/RsCoEawrJC/merge.a.vcf.gz /tmp/RsCoEawrJC/merge.b.vcf.gz /tmp/RsCoEawrJC/merge.c.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge --no-version --force-samples -Fx /tmp/0aIugS0D6E/merge.a.vcf.gz /tmp/0aIugS0D6E/merge.b.vcf.gz /tmp/0aIugS0D6E/merge.c.vcf.gz + /build/bcftools-1.9/bcftools merge --no-version --force-samples -Fx /tmp/RsCoEawrJC/merge.a.vcf.gz /tmp/RsCoEawrJC/merge.b.vcf.gz /tmp/RsCoEawrJC/merge.c.vcf.gz .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge -Ob --force-samples -Fx /tmp/0aIugS0D6E/merge.a.vcf.gz /tmp/0aIugS0D6E/merge.b.vcf.gz /tmp/0aIugS0D6E/merge.c.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools merge -Ob --force-samples -Fx /tmp/RsCoEawrJC/merge.a.vcf.gz /tmp/RsCoEawrJC/merge.b.vcf.gz /tmp/RsCoEawrJC/merge.c.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge --no-version --force-samples -0 /tmp/0aIugS0D6E/merge.a.vcf.gz /tmp/0aIugS0D6E/merge.b.vcf.gz /tmp/0aIugS0D6E/merge.c.vcf.gz + /build/bcftools-1.9/bcftools merge --no-version --force-samples -0 /tmp/RsCoEawrJC/merge.a.vcf.gz /tmp/RsCoEawrJC/merge.b.vcf.gz /tmp/RsCoEawrJC/merge.c.vcf.gz .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge -Ob --force-samples -0 /tmp/0aIugS0D6E/merge.a.vcf.gz /tmp/0aIugS0D6E/merge.b.vcf.gz /tmp/0aIugS0D6E/merge.c.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools merge -Ob --force-samples -0 /tmp/RsCoEawrJC/merge.a.vcf.gz /tmp/RsCoEawrJC/merge.b.vcf.gz /tmp/RsCoEawrJC/merge.c.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge --no-version --force-samples -m none /tmp/0aIugS0D6E/merge.2.a.vcf.gz /tmp/0aIugS0D6E/merge.2.b.vcf.gz + /build/bcftools-1.9/bcftools merge --no-version --force-samples -m none /tmp/RsCoEawrJC/merge.2.a.vcf.gz /tmp/RsCoEawrJC/merge.2.b.vcf.gz .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge -Ob --force-samples -m none /tmp/0aIugS0D6E/merge.2.a.vcf.gz /tmp/0aIugS0D6E/merge.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools merge -Ob --force-samples -m none /tmp/RsCoEawrJC/merge.2.a.vcf.gz /tmp/RsCoEawrJC/merge.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge --no-version --force-samples -m both /tmp/0aIugS0D6E/merge.2.a.vcf.gz /tmp/0aIugS0D6E/merge.2.b.vcf.gz + /build/bcftools-1.9/bcftools merge --no-version --force-samples -m both /tmp/RsCoEawrJC/merge.2.a.vcf.gz /tmp/RsCoEawrJC/merge.2.b.vcf.gz .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge -Ob --force-samples -m both /tmp/0aIugS0D6E/merge.2.a.vcf.gz /tmp/0aIugS0D6E/merge.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools merge -Ob --force-samples -m both /tmp/RsCoEawrJC/merge.2.a.vcf.gz /tmp/RsCoEawrJC/merge.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge --no-version --force-samples -m all /tmp/0aIugS0D6E/merge.2.a.vcf.gz /tmp/0aIugS0D6E/merge.2.b.vcf.gz + /build/bcftools-1.9/bcftools merge --no-version --force-samples -m all /tmp/RsCoEawrJC/merge.2.a.vcf.gz /tmp/RsCoEawrJC/merge.2.b.vcf.gz .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge -Ob --force-samples -m all /tmp/0aIugS0D6E/merge.2.a.vcf.gz /tmp/0aIugS0D6E/merge.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools merge -Ob --force-samples -m all /tmp/RsCoEawrJC/merge.2.a.vcf.gz /tmp/RsCoEawrJC/merge.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/0aIugS0D6E/merge.3.a.vcf.gz /tmp/0aIugS0D6E/merge.3.b.vcf.gz + /build/bcftools-1.9/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/RsCoEawrJC/merge.3.a.vcf.gz /tmp/RsCoEawrJC/merge.3.b.vcf.gz .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/0aIugS0D6E/merge.3.a.vcf.gz /tmp/0aIugS0D6E/merge.3.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/RsCoEawrJC/merge.3.a.vcf.gz /tmp/RsCoEawrJC/merge.3.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge --no-version --force-samples -m id /tmp/0aIugS0D6E/merge.4.a.vcf.gz /tmp/0aIugS0D6E/merge.4.b.vcf.gz + /build/bcftools-1.9/bcftools merge --no-version --force-samples -m id /tmp/RsCoEawrJC/merge.4.a.vcf.gz /tmp/RsCoEawrJC/merge.4.b.vcf.gz .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge -Ob --force-samples -m id /tmp/0aIugS0D6E/merge.4.a.vcf.gz /tmp/0aIugS0D6E/merge.4.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools merge -Ob --force-samples -m id /tmp/RsCoEawrJC/merge.4.a.vcf.gz /tmp/RsCoEawrJC/merge.4.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge --no-version --gvcf - /tmp/0aIugS0D6E/gvcf.merge.1.vcf.gz /tmp/0aIugS0D6E/gvcf.merge.2.vcf.gz /tmp/0aIugS0D6E/gvcf.merge.3.vcf.gz + /build/bcftools-1.9/bcftools merge --no-version --gvcf - /tmp/RsCoEawrJC/gvcf.merge.1.vcf.gz /tmp/RsCoEawrJC/gvcf.merge.2.vcf.gz /tmp/RsCoEawrJC/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/0aIugS0D6E/gvcf.merge.1.vcf.gz /tmp/0aIugS0D6E/gvcf.merge.2.vcf.gz /tmp/0aIugS0D6E/gvcf.merge.3.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/RsCoEawrJC/gvcf.merge.1.vcf.gz /tmp/RsCoEawrJC/gvcf.merge.2.vcf.gz /tmp/RsCoEawrJC/gvcf.merge.3.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge --no-version --gvcf - /tmp/0aIugS0D6E/merge.gvcf.2.a.vcf.gz /tmp/0aIugS0D6E/merge.gvcf.2.b.vcf.gz /tmp/0aIugS0D6E/merge.gvcf.2.c.vcf.gz + /build/bcftools-1.9/bcftools merge --no-version --gvcf - /tmp/RsCoEawrJC/merge.gvcf.2.a.vcf.gz /tmp/RsCoEawrJC/merge.gvcf.2.b.vcf.gz /tmp/RsCoEawrJC/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/0aIugS0D6E/merge.gvcf.2.a.vcf.gz /tmp/0aIugS0D6E/merge.gvcf.2.b.vcf.gz /tmp/0aIugS0D6E/merge.gvcf.2.c.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/RsCoEawrJC/merge.gvcf.2.a.vcf.gz /tmp/RsCoEawrJC/merge.gvcf.2.b.vcf.gz /tmp/RsCoEawrJC/merge.gvcf.2.c.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge --no-version --gvcf - -i SRC:join /tmp/0aIugS0D6E/merge.gvcf.3.a.vcf.gz /tmp/0aIugS0D6E/merge.gvcf.3.b.vcf.gz + /build/bcftools-1.9/bcftools merge --no-version --gvcf - -i SRC:join /tmp/RsCoEawrJC/merge.gvcf.3.a.vcf.gz /tmp/RsCoEawrJC/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge -Ob --gvcf - -i SRC:join /tmp/0aIugS0D6E/merge.gvcf.3.a.vcf.gz /tmp/0aIugS0D6E/merge.gvcf.3.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools merge -Ob --gvcf - -i SRC:join /tmp/RsCoEawrJC/merge.gvcf.3.a.vcf.gz /tmp/RsCoEawrJC/merge.gvcf.3.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge --no-version /tmp/0aIugS0D6E/merge.5.a.vcf.gz /tmp/0aIugS0D6E/merge.5.b.vcf.gz + /build/bcftools-1.9/bcftools merge --no-version /tmp/RsCoEawrJC/merge.5.a.vcf.gz /tmp/RsCoEawrJC/merge.5.b.vcf.gz .. ok test_vcf_merge: - /build/bcftools-1.9/bcftools merge -Ob /tmp/0aIugS0D6E/merge.5.a.vcf.gz /tmp/0aIugS0D6E/merge.5.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools merge -Ob /tmp/RsCoEawrJC/merge.5.a.vcf.gz /tmp/RsCoEawrJC/merge.5.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/0aIugS0D6E/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' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/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' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XRI\n' -i'XRI[*]>1111' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/0aIugS0D6E/query.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/0aIugS0D6E/query.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/0aIugS0D6E/query.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/0aIugS0D6E/query.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/0aIugS0D6E/query.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/0aIugS0D6E/query.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/0aIugS0D6E/query.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/0aIugS0D6E/query.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/0aIugS0D6E/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' /tmp/RsCoEawrJC/view.vectors.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/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' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.vectors.vcf.gz | /build/bcftools-1.9/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/0aIugS0D6E/query.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/RsCoEawrJC/query.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/0aIugS0D6E/query.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/RsCoEawrJC/query.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/0aIugS0D6E/query.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/RsCoEawrJC/query.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/0aIugS0D6E/query.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/RsCoEawrJC/query.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/0aIugS0D6E/query.2.vcf.gz + /build/bcftools-1.9/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/RsCoEawrJC/query.2.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.2.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.2.vcf.gz | /build/bcftools-1.9/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'IINT="."' -f'%POS %IINT\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'IINT!="."' -f'%POS %IINT\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'IINT!="."' -f'%POS %IINT\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'IINT="."' -f'%POS %IINT\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%LINE' /tmp/0aIugS0D6E/query.vcf.gz + /build/bcftools-1.9/bcftools query -f'%LINE' /tmp/RsCoEawrJC/query.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%LINE' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.vcf.gz | /build/bcftools-1.9/bcftools query -f'%LINE' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/0aIugS0D6E/query.filter-type.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/RsCoEawrJC/query.filter-type.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.filter-type.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter-type.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/0aIugS0D6E/query.filter-type.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/RsCoEawrJC/query.filter-type.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.filter-type.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter-type.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/0aIugS0D6E/query.filter-type.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/RsCoEawrJC/query.filter-type.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.filter-type.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter-type.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/0aIugS0D6E/query.filter-type.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/RsCoEawrJC/query.filter-type.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.filter-type.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter-type.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/0aIugS0D6E/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' /tmp/RsCoEawrJC/filter-missing-floats.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/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' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/filter-missing-floats.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/0aIugS0D6E/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' /tmp/RsCoEawrJC/filter-missing-floats.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/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' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/filter-missing-floats.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/0aIugS0D6E/missing.vcf.gz + /build/bcftools-1.9/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/RsCoEawrJC/missing.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/missing.vcf.gz | /build/bcftools-1.9/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/0aIugS0D6E/query.filter.2.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/RsCoEawrJC/query.filter.2.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.filter.2.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.2.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/0aIugS0D6E/filter.5.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/RsCoEawrJC/filter.5.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/filter.5.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/filter.5.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/0aIugS0D6E/filter.5.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/RsCoEawrJC/filter.5.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/filter.5.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/filter.5.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.filter.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/0aIugS0D6E/query.filter.3.vcf.gz + /build/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/RsCoEawrJC/query.filter.3.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.filter.3.vcf.gz | /build/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.3.vcf.gz | /build/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/0aIugS0D6E/query.filter.3.vcf.gz + /build/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/RsCoEawrJC/query.filter.3.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.filter.3.vcf.gz | /build/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.3.vcf.gz | /build/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/0aIugS0D6E/query.filter.3.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/RsCoEawrJC/query.filter.3.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.filter.3.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.3.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/0aIugS0D6E/query.filter.4.vcf.gz + /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/RsCoEawrJC/query.filter.4.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/query.filter.4.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.4.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.9/test/query.56.out' /tmp/0aIugS0D6E/view.vcf.gz + /build/bcftools-1.9/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.9/test/query.56.out' /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.vcf.gz | /build/bcftools-1.9/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.9/test/query.56.out' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.9/test/query.56.out' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/0aIugS0D6E/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' /tmp/RsCoEawrJC/query.filter.5.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/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' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.5.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/0aIugS0D6E/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' /tmp/RsCoEawrJC/query.filter.5.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/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' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.5.vcf.gz | /build/bcftools-1.9/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' .. ok test_vcf_query: - /build/bcftools-1.9/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/0aIugS0D6E/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' /tmp/RsCoEawrJC/query.filter.5.vcf.gz .. ok test_vcf_query: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/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' + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/query.filter.5.vcf.gz | /build/bcftools-1.9/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -cx -f /build/bcftools-1.9/test/norm.fa /tmp/0aIugS0D6E/norm.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -cx -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -cx -f /build/bcftools-1.9/test/norm.fa /tmp/0aIugS0D6E/norm.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -cx -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -m- /tmp/0aIugS0D6E/norm.split.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -m- /tmp/RsCoEawrJC/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -m- /tmp/0aIugS0D6E/norm.split.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -m- /tmp/RsCoEawrJC/norm.split.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -m- /tmp/0aIugS0D6E/norm.split.2.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -m- /tmp/RsCoEawrJC/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -m- /tmp/0aIugS0D6E/norm.split.2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -m- /tmp/RsCoEawrJC/norm.split.2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -m- -f /build/bcftools-1.9/test/norm.fa /tmp/0aIugS0D6E/norm.split.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -m- -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -m- -f /build/bcftools-1.9/test/norm.fa /tmp/0aIugS0D6E/norm.split.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -m- -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.split.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -m+ /tmp/0aIugS0D6E/norm.merge.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -m+ /tmp/RsCoEawrJC/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/0aIugS0D6E/norm.merge.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/RsCoEawrJC/norm.merge.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -m+ /tmp/0aIugS0D6E/norm.merge.2.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -m+ /tmp/RsCoEawrJC/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/0aIugS0D6E/norm.merge.2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/RsCoEawrJC/norm.merge.2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -m+ /tmp/0aIugS0D6E/norm.merge.3.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -m+ /tmp/RsCoEawrJC/norm.merge.3.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/0aIugS0D6E/norm.merge.3.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/RsCoEawrJC/norm.merge.3.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -m+ -s /tmp/0aIugS0D6E/norm.merge.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -m+ -s /tmp/RsCoEawrJC/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -m+ -s /tmp/0aIugS0D6E/norm.merge.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -m+ -s /tmp/RsCoEawrJC/norm.merge.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -Nc s -f /build/bcftools-1.9/test/norm.fa /tmp/0aIugS0D6E/norm.setref.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -Nc s -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.setref.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -Nc s -f /build/bcftools-1.9/test/norm.fa /tmp/0aIugS0D6E/norm.setref.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -Nc s -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.setref.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -f /build/bcftools-1.9/test/norm.fa /tmp/0aIugS0D6E/norm.telomere.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.telomere.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -f /build/bcftools-1.9/test/norm.fa /tmp/0aIugS0D6E/norm.telomere.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -f /build/bcftools-1.9/test/norm.fa /tmp/RsCoEawrJC/norm.telomere.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -d snps /tmp/0aIugS0D6E/norm.rmdup.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -d snps /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -d snps /tmp/0aIugS0D6E/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -d snps /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -d indels /tmp/0aIugS0D6E/norm.rmdup.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -d indels /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -d indels /tmp/0aIugS0D6E/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -d indels /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -d both /tmp/0aIugS0D6E/norm.rmdup.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -d both /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -d both /tmp/0aIugS0D6E/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -d both /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -d all /tmp/0aIugS0D6E/norm.rmdup.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -d all /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -d all /tmp/0aIugS0D6E/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -d all /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm --no-version -d none /tmp/0aIugS0D6E/norm.rmdup.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools norm --no-version -d none /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: - /build/bcftools-1.9/bcftools norm -Ob -d none /tmp/0aIugS0D6E/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools norm -Ob -d none /tmp/RsCoEawrJC/norm.rmdup.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/0aIugS0D6E/view.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/0aIugS0D6E/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -f PASS -Xks NA00003 /tmp/0aIugS0D6E/view.vcf.gz -r20,Y + /build/bcftools-1.9/bcftools view --no-version -f PASS -Xks NA00003 /tmp/RsCoEawrJC/view.vcf.gz -r20,Y .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -f PASS -Xks NA00003 /tmp/0aIugS0D6E/view.vcf.gz -r20,Y | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -f PASS -Xks NA00003 /tmp/RsCoEawrJC/view.vcf.gz -r20,Y | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -xs NA00003 /tmp/0aIugS0D6E/view.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -xs NA00003 /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -xs NA00003 /tmp/0aIugS0D6E/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -xs NA00003 /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/0aIugS0D6E/view.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/0aIugS0D6E/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -p /tmp/0aIugS0D6E/view.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -p /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -p /tmp/0aIugS0D6E/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -p /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -P /tmp/0aIugS0D6E/view.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -P /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -P /tmp/0aIugS0D6E/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -P /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/0aIugS0D6E/view.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/0aIugS0D6E/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -Hu /tmp/0aIugS0D6E/view.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -Hu /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -GVsnps /tmp/0aIugS0D6E/view.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -GVsnps /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -GVsnps /tmp/0aIugS0D6E/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -GVsnps /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/0aIugS0D6E/view.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/0aIugS0D6E/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -s ^NA00003 /tmp/0aIugS0D6E/view.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -s ^NA00003 /tmp/RsCoEawrJC/view.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -s ^NA00003 /tmp/0aIugS0D6E/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -s ^NA00003 /tmp/RsCoEawrJC/view.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version /tmp/0aIugS0D6E/view.omitgenotypes.vcf.gz + /build/bcftools-1.9/bcftools view --no-version /tmp/RsCoEawrJC/view.omitgenotypes.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/view.omitgenotypes.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/view.omitgenotypes.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -G /tmp/0aIugS0D6E/view.omitgenotypes.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -G /tmp/RsCoEawrJC/view.omitgenotypes.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -G /tmp/0aIugS0D6E/view.omitgenotypes.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -G /tmp/RsCoEawrJC/view.omitgenotypes.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -HG /tmp/0aIugS0D6E/view.omitgenotypes.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -HG /tmp/RsCoEawrJC/view.omitgenotypes.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -a /tmp/0aIugS0D6E/many.alleles.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -a /tmp/RsCoEawrJC/many.alleles.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -a /tmp/0aIugS0D6E/many.alleles.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -a /tmp/RsCoEawrJC/many.alleles.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -asA /tmp/0aIugS0D6E/view.vectors.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -asA /tmp/RsCoEawrJC/view.vectors.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -asA /tmp/0aIugS0D6E/view.vectors.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -asA /tmp/RsCoEawrJC/view.vectors.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -asB /tmp/0aIugS0D6E/view.vectors.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -asB /tmp/RsCoEawrJC/view.vectors.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -asB /tmp/0aIugS0D6E/view.vectors.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -asB /tmp/RsCoEawrJC/view.vectors.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -asA /tmp/0aIugS0D6E/view.vectors.2.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -asA /tmp/RsCoEawrJC/view.vectors.2.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -asA /tmp/0aIugS0D6E/view.vectors.2.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -asA /tmp/RsCoEawrJC/view.vectors.2.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -H -i'TXT0="text"' /tmp/0aIugS0D6E/view.filter.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -H -i'TXT0="text"' /tmp/RsCoEawrJC/view.filter.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -T /build/bcftools-1.9/test/view.chrs.tab /tmp/0aIugS0D6E/view.chrs.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -T /build/bcftools-1.9/test/view.chrs.tab /tmp/RsCoEawrJC/view.chrs.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -T /build/bcftools-1.9/test/view.chrs.tab /tmp/0aIugS0D6E/view.chrs.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -T /build/bcftools-1.9/test/view.chrs.tab /tmp/RsCoEawrJC/view.chrs.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -i 'POS>=3062917' /tmp/0aIugS0D6E/filter.2.vcf.gz 1:3062917-3157410 + /build/bcftools-1.9/bcftools view --no-version -i 'POS>=3062917' /tmp/RsCoEawrJC/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view -Ob -i 'POS>=3062917' /tmp/0aIugS0D6E/filter.2.vcf.gz 1:3062917-3157410 | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools view -Ob -i 'POS>=3062917' /tmp/RsCoEawrJC/filter.2.vcf.gz 1:3062917-3157410 | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: @@ -1997,27 +2031,27 @@ .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -H -C5:nonmajor /tmp/0aIugS0D6E/view.minmaxac.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -H -C5:nonmajor /tmp/RsCoEawrJC/view.minmaxac.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -H -c6:nonmajor /tmp/0aIugS0D6E/view.minmaxac.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -H -c6:nonmajor /tmp/RsCoEawrJC/view.minmaxac.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -H -q0.3:major /tmp/0aIugS0D6E/view.minmaxac.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -H -q0.3:major /tmp/RsCoEawrJC/view.minmaxac.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/0aIugS0D6E/view.filter.annovar.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/RsCoEawrJC/view.filter.annovar.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/0aIugS0D6E/view.filter.annovar.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/RsCoEawrJC/view.filter.annovar.vcf.gz .. ok test_vcf_view: - /build/bcftools-1.9/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/0aIugS0D6E/view.filter.annovar.vcf.gz + /build/bcftools-1.9/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/RsCoEawrJC/view.filter.annovar.vcf.gz .. ok test_vcf_call: @@ -2061,11 +2095,11 @@ .. ok test_vcf_call_cAls: - /build/bcftools-1.9/bcftools call --no-version -mA -C alleles -T /tmp/0aIugS0D6E/mpileup.tab.gz /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null + /build/bcftools-1.9/bcftools call --no-version -mA -C alleles -T /tmp/RsCoEawrJC/mpileup.tab.gz /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call_cAls: - /build/bcftools-1.9/bcftools call -Ob -mA -C alleles -T /tmp/0aIugS0D6E/mpileup.tab.gz /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools call -Ob -mA -C alleles -T /tmp/RsCoEawrJC/mpileup.tab.gz /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: @@ -2390,7 +2424,7 @@ 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.vG9Odk +Writing to /tmp/bcftools-sort.BAdACk Merging 17 temporary files Cleaning Done @@ -2398,7 +2432,7 @@ 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.12XyHf +Writing to /tmp/bcftools-sort.V42Xro Merging 17 temporary files Cleaning Done @@ -2406,7 +2440,7 @@ 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.vOJKBs +Writing to /tmp/bcftools-sort.d0malH Merging 3 temporary files Cleaning Done @@ -2414,98 +2448,98 @@ 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.8nYnYs +Writing to /tmp/bcftools-sort.KomGgU Merging 3 temporary files Cleaning Done .. ok test_vcf_regions: - /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.9/test/regions.tab /tmp/0aIugS0D6E/regions.vcf.gz + /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.9/test/regions.tab /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.9/test/regions.tab + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.9/test/regions.tab .. ok test_vcf_regions: - /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/bcftools-1.9/test/regions.tab /tmp/0aIugS0D6E/regions.vcf.gz + /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/bcftools-1.9/test/regions.tab /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: - /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/0aIugS0D6E/regions.tab.gz /tmp/0aIugS0D6E/regions.vcf.gz + /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/RsCoEawrJC/regions.tab.gz /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/0aIugS0D6E/regions.tab.gz + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/RsCoEawrJC/regions.tab.gz .. ok test_vcf_regions: - /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/0aIugS0D6E/regions.tab.gz /tmp/0aIugS0D6E/regions.vcf.gz + /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/RsCoEawrJC/regions.tab.gz /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: - /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/0aIugS0D6E/regions.bed /tmp/0aIugS0D6E/regions.vcf.gz + /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/RsCoEawrJC/regions.bed /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/0aIugS0D6E/regions.bed + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/RsCoEawrJC/regions.bed .. ok test_vcf_regions: - /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/0aIugS0D6E/regions.bed /tmp/0aIugS0D6E/regions.vcf.gz + /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/RsCoEawrJC/regions.bed /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: - /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/0aIugS0D6E/regions.bed.gz /tmp/0aIugS0D6E/regions.vcf.gz + /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/RsCoEawrJC/regions.bed.gz /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_regions: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/0aIugS0D6E/regions.bed.gz + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/RsCoEawrJC/regions.bed.gz .. ok test_vcf_regions: - /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/0aIugS0D6E/regions.bed.gz /tmp/0aIugS0D6E/regions.vcf.gz + /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/RsCoEawrJC/regions.bed.gz /tmp/RsCoEawrJC/regions.vcf.gz .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annotate.tab.gz -h /build/bcftools-1.9/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-1.9/test/annotate.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annotate.tab.gz -h /build/bcftools-1.9/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-1.9/test/annotate.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annotate2.tab.gz -h /build/bcftools-1.9/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-1.9/test/annotate.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annotate2.tab.gz -h /build/bcftools-1.9/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-1.9/test/annotate.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/0aIugS0D6E/annotate.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/RsCoEawrJC/annotate.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/0aIugS0D6E/annotate.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/RsCoEawrJC/annotate.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/0aIugS0D6E/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/0aIugS0D6E/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/0aIugS0D6E/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/0aIugS0D6E/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: @@ -2525,480 +2559,480 @@ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/annots4.vcf.gz -c +INFO /tmp/0aIugS0D6E/annotate4.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots4.vcf.gz -c +INFO /tmp/RsCoEawrJC/annotate4.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/annots4.vcf.gz -c +INFO /tmp/0aIugS0D6E/annotate4.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots4.vcf.gz -c +INFO /tmp/RsCoEawrJC/annotate4.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots4.tab.gz -h /build/bcftools-1.9/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-1.9/test/annotate4.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots4.tab.gz -h /build/bcftools-1.9/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-1.9/test/annotate4.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots10.tab.gz -h /build/bcftools-1.9/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-1.9/test/annotate10.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots10.tab.gz -h /build/bcftools-1.9/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-1.9/test/annotate10.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/0aIugS0D6E/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/0aIugS0D6E/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-1.9/test/annotate2.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-1.9/test/annotate2.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/0aIugS0D6E/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/0aIugS0D6E/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/0aIugS0D6E/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/0aIugS0D6E/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/0aIugS0D6E/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/0aIugS0D6E/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/RsCoEawrJC/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/annots11.vcf.gz -c FMT /tmp/0aIugS0D6E/annotate11.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots11.vcf.gz -c FMT /tmp/RsCoEawrJC/annotate11.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/annots11.vcf.gz -c FMT /tmp/0aIugS0D6E/annotate11.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots11.vcf.gz -c FMT /tmp/RsCoEawrJC/annotate11.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +missing2ref --no-version /tmp/0aIugS0D6E/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +missing2ref --no-version /tmp/RsCoEawrJC/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +missing2ref --no-version /tmp/0aIugS0D6E/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +missing2ref --no-version /tmp/RsCoEawrJC/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +setGT --no-version /tmp/0aIugS0D6E/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +setGT --no-version /tmp/0aIugS0D6E/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +setGT --no-version /tmp/0aIugS0D6E/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +setGT --no-version /tmp/0aIugS0D6E/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +setGT --no-version /tmp/0aIugS0D6E/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/build/bcftools-1.9/test/setGT.samples.txt]="het"' 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/build/bcftools-1.9/test/setGT.samples.txt]="het"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +setGT --no-version /tmp/0aIugS0D6E/setGT.2.bcf -- -t q -n . -i 'GT[@/build/bcftools-1.9/test/setGT.samples.txt]="het"' 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/setGT.2.bcf -- -t q -n . -i 'GT[@/build/bcftools-1.9/test/setGT.samples.txt]="het"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +setGT --no-version /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/build/bcftools-1.9/test/setGT.samples.txt]="het" & binom(AD[@/build/bcftools-1.9/test/setGT.samples.txt])<0.1' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +setGT --no-version /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools +setGT --no-version /tmp/RsCoEawrJC/setGT.2.bcf -- -t q -n . -i 'GT[@/build/bcftools-1.9/test/setGT.samples.txt]="het" & binom(AD[@/build/bcftools-1.9/test/setGT.samples.txt])<0.1' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -a /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools annotate -a /tmp/RsCoEawrJC/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-1.9/test/annotate9.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools annotate -Ob -a /tmp/RsCoEawrJC/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-1.9/test/annotate9.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-AN-AC --no-version /tmp/0aIugS0D6E/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-AN-AC --no-version /tmp/RsCoEawrJC/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-AN-AC --no-version /tmp/0aIugS0D6E/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-AN-AC --no-version /tmp/RsCoEawrJC/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +dosage /tmp/0aIugS0D6E/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +dosage /tmp/RsCoEawrJC/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +dosage /tmp/0aIugS0D6E/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +dosage /tmp/RsCoEawrJC/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fixploidy --no-version /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools +fixploidy --no-version /tmp/RsCoEawrJC/fixploidy.vcf.gz -- -s /build/bcftools-1.9/test/fixploidy.samples -p /build/bcftools-1.9/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fixploidy --no-version /tmp/0aIugS0D6E/fixploidy.bcf -- -s /build/bcftools-1.9/test/fixploidy.samples -p /build/bcftools-1.9/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fixploidy --no-version /tmp/RsCoEawrJC/fixploidy.bcf -- -s /build/bcftools-1.9/test/fixploidy.samples -p /build/bcftools-1.9/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +guess-ploidy /tmp/0aIugS0D6E/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +guess-ploidy /tmp/RsCoEawrJC/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +guess-ploidy /tmp/0aIugS0D6E/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +guess-ploidy /tmp/RsCoEawrJC/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +guess-ploidy /tmp/0aIugS0D6E/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +guess-ploidy /tmp/RsCoEawrJC/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ Warning: PL tag not found in header, switching to GL .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +guess-ploidy /tmp/0aIugS0D6E/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +guess-ploidy /tmp/RsCoEawrJC/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ Warning: PL tag not found in header, switching to GL .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +tag2tag --no-version /tmp/0aIugS0D6E/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +tag2tag --no-version /tmp/RsCoEawrJC/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +tag2tag --no-version /tmp/0aIugS0D6E/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +tag2tag --no-version /tmp/RsCoEawrJC/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +tag2tag --no-version /tmp/0aIugS0D6E/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +tag2tag --no-version /tmp/RsCoEawrJC/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +tag2tag --no-version /tmp/0aIugS0D6E/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +tag2tag --no-version /tmp/RsCoEawrJC/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/0aIugS0D6E/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/0aIugS0D6E/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/0aIugS0D6E/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/0aIugS0D6E/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/0aIugS0D6E/view.vcf.gz -- -t AC -S /build/bcftools-1.9/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/view.vcf.gz -- -t AC -S /build/bcftools-1.9/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/0aIugS0D6E/view.bcf -- -t AC -S /build/bcftools-1.9/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/view.bcf -- -t AC -S /build/bcftools-1.9/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/0aIugS0D6E/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/0aIugS0D6E/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/0aIugS0D6E/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/0aIugS0D6E/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/RsCoEawrJC/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTisec /tmp/0aIugS0D6E/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTisec /tmp/RsCoEawrJC/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +trio-switch-rate /tmp/0aIugS0D6E/trio.vcf.gz -- -p /build/bcftools-1.9/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +trio-switch-rate /tmp/RsCoEawrJC/trio.vcf.gz -- -p /build/bcftools-1.9/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +trio-switch-rate /tmp/0aIugS0D6E/trio.bcf -- -p /build/bcftools-1.9/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +trio-switch-rate /tmp/RsCoEawrJC/trio.bcf -- -p /build/bcftools-1.9/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +trio-stats /tmp/0aIugS0D6E/trio-stats.vcf.gz -p /build/bcftools-1.9/test/trio-stats.ped | grep -v ^CMD 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +trio-stats /tmp/RsCoEawrJC/trio-stats.vcf.gz -p /build/bcftools-1.9/test/trio-stats.ped | grep -v ^CMD 2>/dev/null | grep -v ^##bcftools_ Identified 2 complete trios in the VCF file .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +trio-stats /tmp/0aIugS0D6E/trio-stats.bcf -p /build/bcftools-1.9/test/trio-stats.ped | grep -v ^CMD 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +trio-stats /tmp/RsCoEawrJC/trio-stats.bcf -p /build/bcftools-1.9/test/trio-stats.ped | grep -v ^CMD 2>/dev/null | grep -v ^##bcftools_ Identified 2 complete trios in the VCF file .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +ad-bias /tmp/0aIugS0D6E/ad-bias.vcf.gz -- -s /build/bcftools-1.9/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +ad-bias /tmp/RsCoEawrJC/ad-bias.vcf.gz -- -s /build/bcftools-1.9/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +ad-bias /tmp/0aIugS0D6E/ad-bias.bcf -- -s /build/bcftools-1.9/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +ad-bias /tmp/RsCoEawrJC/ad-bias.bcf -- -s /build/bcftools-1.9/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +af-dist /tmp/0aIugS0D6E/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +af-dist /tmp/RsCoEawrJC/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +af-dist /tmp/0aIugS0D6E/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +af-dist /tmp/RsCoEawrJC/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fixref /tmp/0aIugS0D6E/fixref.2a.vcf.gz -- -f /build/bcftools-1.9/test/norm.fa -i /tmp/0aIugS0D6E/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fixref /tmp/RsCoEawrJC/fixref.2a.vcf.gz -- -f /build/bcftools-1.9/test/norm.fa -i /tmp/RsCoEawrJC/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fixref /tmp/0aIugS0D6E/fixref.2a.bcf -- -f /build/bcftools-1.9/test/norm.fa -i /tmp/0aIugS0D6E/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fixref /tmp/RsCoEawrJC/fixref.2a.bcf -- -f /build/bcftools-1.9/test/norm.fa -i /tmp/RsCoEawrJC/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fixref /tmp/0aIugS0D6E/fixref.3.vcf.gz -- -f /build/bcftools-1.9/test/fixref.3.fa -m top 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fixref /tmp/RsCoEawrJC/fixref.3.vcf.gz -- -f /build/bcftools-1.9/test/fixref.3.fa -m top 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fixref /tmp/0aIugS0D6E/fixref.3.bcf -- -f /build/bcftools-1.9/test/fixref.3.fa -m top 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fixref /tmp/RsCoEawrJC/fixref.3.bcf -- -f /build/bcftools-1.9/test/fixref.3.fa -m top 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-from-fasta /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools +fill-from-fasta /tmp/RsCoEawrJC/aa.vcf.gz -- -f /build/bcftools-1.9/test/aa.fa -c AA -h /build/bcftools-1.9/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-from-fasta /tmp/0aIugS0D6E/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_ + /build/bcftools-1.9/bcftools +fill-from-fasta /tmp/RsCoEawrJC/aa.bcf -- -f /build/bcftools-1.9/test/aa.fa -c AA -h /build/bcftools-1.9/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-from-fasta /tmp/0aIugS0D6E/ref.vcf.gz -- -f /build/bcftools-1.9/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-from-fasta /tmp/RsCoEawrJC/ref.vcf.gz -- -f /build/bcftools-1.9/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +fill-from-fasta /tmp/0aIugS0D6E/ref.bcf -- -f /build/bcftools-1.9/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +fill-from-fasta /tmp/RsCoEawrJC/ref.bcf -- -f /build/bcftools-1.9/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/0aIugS0D6E/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/RsCoEawrJC/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/0aIugS0D6E/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/RsCoEawrJC/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/0aIugS0D6E/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/RsCoEawrJC/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/0aIugS0D6E/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/RsCoEawrJC/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/0aIugS0D6E/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/RsCoEawrJC/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/0aIugS0D6E/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/RsCoEawrJC/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +mendelian /tmp/0aIugS0D6E/mendelian.vcf.gz -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +mendelian /tmp/RsCoEawrJC/mendelian.vcf.gz -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +mendelian /tmp/0aIugS0D6E/mendelian.bcf -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +mendelian /tmp/RsCoEawrJC/mendelian.bcf -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +mendelian /tmp/0aIugS0D6E/mendelian.vcf.gz -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +mendelian /tmp/RsCoEawrJC/mendelian.vcf.gz -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +mendelian /tmp/0aIugS0D6E/mendelian.bcf -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +mendelian /tmp/RsCoEawrJC/mendelian.bcf -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +mendelian /tmp/0aIugS0D6E/mendelian.vcf.gz -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +mendelian /tmp/RsCoEawrJC/mendelian.vcf.gz -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +mendelian /tmp/0aIugS0D6E/mendelian.bcf -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +mendelian /tmp/RsCoEawrJC/mendelian.bcf -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +contrast /tmp/0aIugS0D6E/contrast.vcf.gz -0 a,b -1 c 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +contrast /tmp/RsCoEawrJC/contrast.vcf.gz -0 a,b -1 c 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: - /build/bcftools-1.9/bcftools +contrast /tmp/0aIugS0D6E/contrast.bcf -0 a,b -1 c 2>/dev/null | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools +contrast /tmp/RsCoEawrJC/contrast.bcf -0 a,b -1 c 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat --no-version /tmp/0aIugS0D6E/concat.1.a.vcf.gz /tmp/0aIugS0D6E/concat.1.b.vcf.gz + /build/bcftools-1.9/bcftools concat --no-version /tmp/RsCoEawrJC/concat.1.a.vcf.gz /tmp/RsCoEawrJC/concat.1.b.vcf.gz .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat -Ob /tmp/0aIugS0D6E/concat.1.a.vcf.gz /tmp/0aIugS0D6E/concat.1.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools concat -Ob /tmp/RsCoEawrJC/concat.1.a.vcf.gz /tmp/RsCoEawrJC/concat.1.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat --no-version /tmp/0aIugS0D6E/concat.1.a.bcf /tmp/0aIugS0D6E/concat.1.b.bcf + /build/bcftools-1.9/bcftools concat --no-version /tmp/RsCoEawrJC/concat.1.a.bcf /tmp/RsCoEawrJC/concat.1.b.bcf .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat -Ob /tmp/0aIugS0D6E/concat.1.a.bcf /tmp/0aIugS0D6E/concat.1.b.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools concat -Ob /tmp/RsCoEawrJC/concat.1.a.bcf /tmp/RsCoEawrJC/concat.1.b.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat --no-version -a /tmp/0aIugS0D6E/concat.2.a.vcf.gz /tmp/0aIugS0D6E/concat.2.b.vcf.gz + /build/bcftools-1.9/bcftools concat --no-version -a /tmp/RsCoEawrJC/concat.2.a.vcf.gz /tmp/RsCoEawrJC/concat.2.b.vcf.gz .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat -Ob -a /tmp/0aIugS0D6E/concat.2.a.vcf.gz /tmp/0aIugS0D6E/concat.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools concat -Ob -a /tmp/RsCoEawrJC/concat.2.a.vcf.gz /tmp/RsCoEawrJC/concat.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat --no-version -a /tmp/0aIugS0D6E/concat.2.a.bcf /tmp/0aIugS0D6E/concat.2.b.bcf + /build/bcftools-1.9/bcftools concat --no-version -a /tmp/RsCoEawrJC/concat.2.a.bcf /tmp/RsCoEawrJC/concat.2.b.bcf .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat -Ob -a /tmp/0aIugS0D6E/concat.2.a.bcf /tmp/0aIugS0D6E/concat.2.b.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools concat -Ob -a /tmp/RsCoEawrJC/concat.2.a.bcf /tmp/RsCoEawrJC/concat.2.b.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat --no-version -aD /tmp/0aIugS0D6E/concat.2.a.vcf.gz /tmp/0aIugS0D6E/concat.2.b.vcf.gz + /build/bcftools-1.9/bcftools concat --no-version -aD /tmp/RsCoEawrJC/concat.2.a.vcf.gz /tmp/RsCoEawrJC/concat.2.b.vcf.gz .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat -Ob -aD /tmp/0aIugS0D6E/concat.2.a.vcf.gz /tmp/0aIugS0D6E/concat.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools concat -Ob -aD /tmp/RsCoEawrJC/concat.2.a.vcf.gz /tmp/RsCoEawrJC/concat.2.b.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat --no-version -aD /tmp/0aIugS0D6E/concat.2.a.bcf /tmp/0aIugS0D6E/concat.2.b.bcf + /build/bcftools-1.9/bcftools concat --no-version -aD /tmp/RsCoEawrJC/concat.2.a.bcf /tmp/RsCoEawrJC/concat.2.b.bcf .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat -Ob -aD /tmp/0aIugS0D6E/concat.2.a.bcf /tmp/0aIugS0D6E/concat.2.b.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools concat -Ob -aD /tmp/RsCoEawrJC/concat.2.a.bcf /tmp/RsCoEawrJC/concat.2.b.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat --no-version -l /tmp/0aIugS0D6E/concat.3.a.vcf.gz /tmp/0aIugS0D6E/concat.3.b.vcf.gz /tmp/0aIugS0D6E/concat.3.0.vcf.gz /tmp/0aIugS0D6E/concat.3.c.vcf.gz /tmp/0aIugS0D6E/concat.3.d.vcf.gz /tmp/0aIugS0D6E/concat.3.e.vcf.gz /tmp/0aIugS0D6E/concat.3.f.vcf.gz + /build/bcftools-1.9/bcftools concat --no-version -l /tmp/RsCoEawrJC/concat.3.a.vcf.gz /tmp/RsCoEawrJC/concat.3.b.vcf.gz /tmp/RsCoEawrJC/concat.3.0.vcf.gz /tmp/RsCoEawrJC/concat.3.c.vcf.gz /tmp/RsCoEawrJC/concat.3.d.vcf.gz /tmp/RsCoEawrJC/concat.3.e.vcf.gz /tmp/RsCoEawrJC/concat.3.f.vcf.gz .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat -Ob -l /tmp/0aIugS0D6E/concat.3.a.vcf.gz /tmp/0aIugS0D6E/concat.3.b.vcf.gz /tmp/0aIugS0D6E/concat.3.0.vcf.gz /tmp/0aIugS0D6E/concat.3.c.vcf.gz /tmp/0aIugS0D6E/concat.3.d.vcf.gz /tmp/0aIugS0D6E/concat.3.e.vcf.gz /tmp/0aIugS0D6E/concat.3.f.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ + /build/bcftools-1.9/bcftools concat -Ob -l /tmp/RsCoEawrJC/concat.3.a.vcf.gz /tmp/RsCoEawrJC/concat.3.b.vcf.gz /tmp/RsCoEawrJC/concat.3.0.vcf.gz /tmp/RsCoEawrJC/concat.3.c.vcf.gz /tmp/RsCoEawrJC/concat.3.d.vcf.gz /tmp/RsCoEawrJC/concat.3.e.vcf.gz /tmp/RsCoEawrJC/concat.3.f.vcf.gz | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat --no-version -l /tmp/0aIugS0D6E/concat.3.a.bcf /tmp/0aIugS0D6E/concat.3.b.bcf /tmp/0aIugS0D6E/concat.3.0.bcf /tmp/0aIugS0D6E/concat.3.c.bcf /tmp/0aIugS0D6E/concat.3.d.bcf /tmp/0aIugS0D6E/concat.3.e.bcf /tmp/0aIugS0D6E/concat.3.f.bcf + /build/bcftools-1.9/bcftools concat --no-version -l /tmp/RsCoEawrJC/concat.3.a.bcf /tmp/RsCoEawrJC/concat.3.b.bcf /tmp/RsCoEawrJC/concat.3.0.bcf /tmp/RsCoEawrJC/concat.3.c.bcf /tmp/RsCoEawrJC/concat.3.d.bcf /tmp/RsCoEawrJC/concat.3.e.bcf /tmp/RsCoEawrJC/concat.3.f.bcf .. ok test_vcf_concat: - /build/bcftools-1.9/bcftools concat -Ob -l /tmp/0aIugS0D6E/concat.3.a.bcf /tmp/0aIugS0D6E/concat.3.b.bcf /tmp/0aIugS0D6E/concat.3.0.bcf /tmp/0aIugS0D6E/concat.3.c.bcf /tmp/0aIugS0D6E/concat.3.d.bcf /tmp/0aIugS0D6E/concat.3.e.bcf /tmp/0aIugS0D6E/concat.3.f.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ -Random seed for test_naive_concat: 2985474107 + /build/bcftools-1.9/bcftools concat -Ob -l /tmp/RsCoEawrJC/concat.3.a.bcf /tmp/RsCoEawrJC/concat.3.b.bcf /tmp/RsCoEawrJC/concat.3.0.bcf /tmp/RsCoEawrJC/concat.3.c.bcf /tmp/RsCoEawrJC/concat.3.d.bcf /tmp/RsCoEawrJC/concat.3.e.bcf /tmp/RsCoEawrJC/concat.3.f.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ +Random seed for test_naive_concat: 2002330770 .. ok test_naive_concat: - /build/bcftools-1.9/bcftools concat --naive /tmp/0aIugS0D6E/naive_concat.0.bcf /tmp/0aIugS0D6E/naive_concat.1.bcf /tmp/0aIugS0D6E/naive_concat.2.bcf /tmp/0aIugS0D6E/naive_concat.3.bcf /tmp/0aIugS0D6E/naive_concat.4.bcf /tmp/0aIugS0D6E/naive_concat.5.bcf /tmp/0aIugS0D6E/naive_concat.6.bcf /tmp/0aIugS0D6E/naive_concat.7.bcf /tmp/0aIugS0D6E/naive_concat.8.bcf /tmp/0aIugS0D6E/naive_concat.9.bcf | /build/bcftools-1.9/bcftools view -H + /build/bcftools-1.9/bcftools concat --naive /tmp/RsCoEawrJC/naive_concat.0.bcf /tmp/RsCoEawrJC/naive_concat.1.bcf /tmp/RsCoEawrJC/naive_concat.2.bcf /tmp/RsCoEawrJC/naive_concat.3.bcf /tmp/RsCoEawrJC/naive_concat.4.bcf /tmp/RsCoEawrJC/naive_concat.5.bcf /tmp/RsCoEawrJC/naive_concat.6.bcf /tmp/RsCoEawrJC/naive_concat.7.bcf /tmp/RsCoEawrJC/naive_concat.8.bcf /tmp/RsCoEawrJC/naive_concat.9.bcf | /build/bcftools-1.9/bcftools view -H .. ok test_naive_concat: - /build/bcftools-1.9/bcftools concat --naive /tmp/0aIugS0D6E/naive_concat.0.vcf.gz /tmp/0aIugS0D6E/naive_concat.1.vcf.gz /tmp/0aIugS0D6E/naive_concat.2.vcf.gz /tmp/0aIugS0D6E/naive_concat.3.vcf.gz /tmp/0aIugS0D6E/naive_concat.4.vcf.gz /tmp/0aIugS0D6E/naive_concat.5.vcf.gz /tmp/0aIugS0D6E/naive_concat.6.vcf.gz /tmp/0aIugS0D6E/naive_concat.7.vcf.gz /tmp/0aIugS0D6E/naive_concat.8.vcf.gz /tmp/0aIugS0D6E/naive_concat.9.vcf.gz | /build/bcftools-1.9/bcftools view -H + /build/bcftools-1.9/bcftools concat --naive /tmp/RsCoEawrJC/naive_concat.0.vcf.gz /tmp/RsCoEawrJC/naive_concat.1.vcf.gz /tmp/RsCoEawrJC/naive_concat.2.vcf.gz /tmp/RsCoEawrJC/naive_concat.3.vcf.gz /tmp/RsCoEawrJC/naive_concat.4.vcf.gz /tmp/RsCoEawrJC/naive_concat.5.vcf.gz /tmp/RsCoEawrJC/naive_concat.6.vcf.gz /tmp/RsCoEawrJC/naive_concat.7.vcf.gz /tmp/RsCoEawrJC/naive_concat.8.vcf.gz /tmp/RsCoEawrJC/naive_concat.9.vcf.gz | /build/bcftools-1.9/bcftools view -H .. ok test_vcf_reheader: @@ -3010,19 +3044,19 @@ .. ok test_vcf_reheader: - /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr /tmp/0aIugS0D6E/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version + /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/0aIugS0D6E/reheader.bcf | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr | /build/bcftools-1.9/bcftools view --no-version + cat /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr /tmp/0aIugS0D6E/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version + /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/0aIugS0D6E/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 + cat /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: @@ -3034,19 +3068,19 @@ .. ok test_vcf_reheader: - /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples /tmp/0aIugS0D6E/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version + /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/0aIugS0D6E/reheader.bcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples | /build/bcftools-1.9/bcftools view --no-version + cat /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples /tmp/0aIugS0D6E/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version + /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/0aIugS0D6E/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 + cat /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: @@ -3058,19 +3092,19 @@ .. ok test_vcf_reheader: - /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 /tmp/0aIugS0D6E/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version + /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/0aIugS0D6E/reheader.bcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 | /build/bcftools-1.9/bcftools view --no-version + cat /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 /tmp/0aIugS0D6E/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version + /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/0aIugS0D6E/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 + cat /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: @@ -3082,19 +3116,19 @@ .. ok test_vcf_reheader: - /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 /tmp/0aIugS0D6E/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version + /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/0aIugS0D6E/reheader.bcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 | /build/bcftools-1.9/bcftools view --no-version + cat /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 /tmp/0aIugS0D6E/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version + /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/0aIugS0D6E/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 + cat /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: @@ -3106,19 +3140,19 @@ .. ok test_vcf_reheader: - /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 /tmp/0aIugS0D6E/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version + /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/0aIugS0D6E/reheader.bcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 | /build/bcftools-1.9/bcftools view --no-version + cat /tmp/RsCoEawrJC/reheader.bcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 /tmp/0aIugS0D6E/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version + /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/0aIugS0D6E/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 + cat /tmp/RsCoEawrJC/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: @@ -3130,139 +3164,139 @@ .. ok test_vcf_reheader: - /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr /tmp/0aIugS0D6E/empty.bcf | /build/bcftools-1.9/bcftools view --no-version + /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr /tmp/RsCoEawrJC/empty.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/0aIugS0D6E/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 + cat /tmp/RsCoEawrJC/empty.bcf | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr /tmp/0aIugS0D6E/empty.vcf.gz | /build/bcftools-1.9/bcftools view --no-version + /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr /tmp/RsCoEawrJC/empty.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/0aIugS0D6E/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 + cat /tmp/RsCoEawrJC/empty.vcf.gz | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr | /build/bcftools-1.9/bcftools view --no-version .. ok test_rename_chrs: - /build/bcftools-1.9/bcftools annotate --rename-chrs /tmp/0aIugS0D6E/rename.map -Ov /tmp/0aIugS0D6E/annotate.bcf | /build/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' + /build/bcftools-1.9/bcftools annotate --rename-chrs /tmp/RsCoEawrJC/rename.map -Ov /tmp/RsCoEawrJC/annotate.bcf | /build/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: - /build/bcftools-1.9/bcftools annotate --rename-chrs /tmp/0aIugS0D6E/rename.map -Ob /tmp/0aIugS0D6E/annotate.bcf | /build/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' + /build/bcftools-1.9/bcftools annotate --rename-chrs /tmp/RsCoEawrJC/rename.map -Ob /tmp/RsCoEawrJC/annotate.bcf | /build/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: - /build/bcftools-1.9/bcftools annotate --rename-chrs /tmp/0aIugS0D6E/rename.map -Ov /build/bcftools-1.9/test/annotate.vcf | /build/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' + /build/bcftools-1.9/bcftools annotate --rename-chrs /tmp/RsCoEawrJC/rename.map -Ov /build/bcftools-1.9/test/annotate.vcf | /build/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: - /build/bcftools-1.9/bcftools annotate --rename-chrs /tmp/0aIugS0D6E/rename.map -Ob /build/bcftools-1.9/test/annotate.vcf | /build/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' + /build/bcftools-1.9/bcftools annotate --rename-chrs /tmp/RsCoEawrJC/rename.map -Ob /build/bcftools-1.9/test/annotate.vcf | /build/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert -g -,. /tmp/0aIugS0D6E/convert.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert -g -,. /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert -g .,- /tmp/0aIugS0D6E/convert.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert -g .,- /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert -g -,. --tag PL /tmp/0aIugS0D6E/convert.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert -g -,. --tag PL /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. --tag PL 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. --tag PL 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert -g .,- --tag PL /tmp/0aIugS0D6E/convert.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert -g .,- --tag PL /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- --tag PL 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- --tag PL 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert -g -,. --vcf-ids /tmp/0aIugS0D6E/check.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert -g -,. --vcf-ids /tmp/RsCoEawrJC/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. --vcf-ids 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. --vcf-ids 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert -g .,- --vcf-ids /tmp/0aIugS0D6E/check.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert -g .,- --vcf-ids /tmp/RsCoEawrJC/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- --vcf-ids 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- --vcf-ids 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert -g -,. --chrom /tmp/0aIugS0D6E/check.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert -g -,. --chrom /tmp/RsCoEawrJC/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. --chrom 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. --chrom 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert -g .,- --chrom /tmp/0aIugS0D6E/check.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert -g .,- --chrom /tmp/RsCoEawrJC/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- --chrom 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- --chrom 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert -g -,. --chrom --vcf-ids /tmp/0aIugS0D6E/check.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert -g -,. --chrom --vcf-ids /tmp/RsCoEawrJC/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert -g .,- --chrom --vcf-ids /tmp/0aIugS0D6E/check.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert -g .,- --chrom --vcf-ids /tmp/RsCoEawrJC/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/check.vcf.gz | /build/bcftools-1.9/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert -h -,.,. /tmp/0aIugS0D6E/convert.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert -h -,.,. /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -h -,.,. 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -h -,.,. 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert -h .,-,. /tmp/0aIugS0D6E/convert.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert -h .,-,. /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -h .,-,. 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -h .,-,. 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert -h .,.,- /tmp/0aIugS0D6E/convert.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert -h .,.,- /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -h .,.,- 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -h .,.,- 2>/dev/null .. ok test_vcf_convert_hls2vcf: @@ -3282,35 +3316,35 @@ .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert --hapsample -,. /tmp/0aIugS0D6E/convert.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert --hapsample -,. /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/convert.vcf.gz | /build/bcftools-1.9/bcftools convert --hapsample -,. 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert --hapsample -,. 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert --hapsample .,- /tmp/0aIugS0D6E/convert.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert --hapsample .,- /tmp/RsCoEawrJC/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/convert.vcf.gz | /build/bcftools-1.9/bcftools convert --hapsample .,- 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.vcf.gz | /build/bcftools-1.9/bcftools convert --hapsample .,- 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools convert --haplegendsample -,.,. /tmp/0aIugS0D6E/convert.hap-missing.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert --haplegendsample -,.,. /tmp/RsCoEawrJC/convert.hap-missing.vcf.gz 2>/dev/null .. ok test_vcf_convert: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/convert.hap-missing.vcf.gz | /build/bcftools-1.9/bcftools convert --haplegendsample -,.,. 2>/dev/null + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.hap-missing.vcf.gz | /build/bcftools-1.9/bcftools convert --haplegendsample -,.,. 2>/dev/null .. ok test_vcf_convert_gvcf: - /build/bcftools-1.9/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.9/test/gvcf.fa /tmp/0aIugS0D6E/convert.gvcf.vcf.gz 2>/dev/null + /build/bcftools-1.9/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.9/test/gvcf.fa /tmp/RsCoEawrJC/convert.gvcf.vcf.gz 2>/dev/null .. ok test_vcf_convert_gvcf: - /build/bcftools-1.9/bcftools view -Ob /tmp/0aIugS0D6E/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 + /build/bcftools-1.9/bcftools view -Ob /tmp/RsCoEawrJC/convert.gvcf.vcf.gz | /build/bcftools-1.9/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.9/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: @@ -3322,51 +3356,51 @@ .. ok test_vcf_consensus: - /build/bcftools-1.9/bcftools consensus /tmp/0aIugS0D6E/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -m /build/bcftools-1.9/test/consensus.tab 2>/dev/null + /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -m /build/bcftools-1.9/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: - /build/bcftools-1.9/bcftools consensus /tmp/0aIugS0D6E/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -m /build/bcftools-1.9/test/consensus.tab -c /tmp/0aIugS0D6E/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/0aIugS0D6E/consensus.1.chain.new + /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -m /build/bcftools-1.9/test/consensus.tab -c /tmp/RsCoEawrJC/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/RsCoEawrJC/consensus.1.chain.new .. ok test_vcf_consensus: - /build/bcftools-1.9/bcftools consensus /tmp/0aIugS0D6E/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 -m /build/bcftools-1.9/test/consensus.tab 2>/dev/null + /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 -m /build/bcftools-1.9/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: - /build/bcftools-1.9/bcftools consensus /tmp/0aIugS0D6E/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 -m /build/bcftools-1.9/test/consensus.tab -c /tmp/0aIugS0D6E/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/0aIugS0D6E/consensus.2.chain.new + /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 -m /build/bcftools-1.9/test/consensus.tab -c /tmp/RsCoEawrJC/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/RsCoEawrJC/consensus.2.chain.new .. ok test_vcf_consensus: - /build/bcftools-1.9/bcftools consensus /tmp/0aIugS0D6E/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -I -m /build/bcftools-1.9/test/consensus.tab 2>/dev/null + /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -I -m /build/bcftools-1.9/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: - /build/bcftools-1.9/bcftools consensus /tmp/0aIugS0D6E/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -I -m /build/bcftools-1.9/test/consensus.tab -c /tmp/0aIugS0D6E/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/0aIugS0D6E/consensus.3.chain.new + /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -I -m /build/bcftools-1.9/test/consensus.tab -c /tmp/RsCoEawrJC/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/RsCoEawrJC/consensus.3.chain.new .. ok test_vcf_consensus: - /build/bcftools-1.9/bcftools consensus /tmp/0aIugS0D6E/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 2>/dev/null + /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 2>/dev/null .. ok test_vcf_consensus_chain: - /build/bcftools-1.9/bcftools consensus /tmp/0aIugS0D6E/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 -c /tmp/0aIugS0D6E/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/0aIugS0D6E/consensus.4.chain.new + /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 -c /tmp/RsCoEawrJC/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/RsCoEawrJC/consensus.4.chain.new .. ok test_vcf_consensus: - /build/bcftools-1.9/bcftools consensus /tmp/0aIugS0D6E/consensus2.vcf.gz -f /build/bcftools-1.9/test/consensus2.fa -H 1 2>/dev/null + /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus2.vcf.gz -f /build/bcftools-1.9/test/consensus2.fa -H 1 2>/dev/null .. ok test_vcf_consensus: - /build/bcftools-1.9/bcftools consensus /tmp/0aIugS0D6E/consensus2.vcf.gz -f /build/bcftools-1.9/test/consensus2.fa -H 2 2>/dev/null + /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus2.vcf.gz -f /build/bcftools-1.9/test/consensus2.fa -H 2 2>/dev/null .. ok test_vcf_consensus: - /build/bcftools-1.9/bcftools consensus /tmp/0aIugS0D6E/empty.vcf.gz -f /build/bcftools-1.9/test/consensus.fa 2>/dev/null + /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/empty.vcf.gz -f /build/bcftools-1.9/test/consensus.fa 2>/dev/null .. ok test_vcf_consensus: - /build/bcftools-1.9/bcftools consensus /tmp/0aIugS0D6E/consensus3.vcf.gz -f /build/bcftools-1.9/test/consensus2.fa -H 2 -M "?" 2>/dev/null + /build/bcftools-1.9/bcftools consensus /tmp/RsCoEawrJC/consensus3.vcf.gz -f /build/bcftools-1.9/test/consensus2.fa -H 2 -M "?" 2>/dev/null .. ok test_mpileup: @@ -3378,11 +3412,11 @@ .. ok test_mpileup: - /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -b /tmp/0aIugS0D6E/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference + /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -b /tmp/RsCoEawrJC/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference .. ok test_mpileup: - /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob -b /tmp/0aIugS0D6E/mpileup.bam.urllist 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference + /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob -b /tmp/RsCoEawrJC/mpileup.bam.urllist 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: @@ -3394,11 +3428,11 @@ .. ok test_mpileup: - /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -b /tmp/0aIugS0D6E/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference + /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -b /tmp/RsCoEawrJC/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference .. ok test_mpileup: - /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob -b /tmp/0aIugS0D6E/mpileup.cram.urllist 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference + /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob -b /tmp/RsCoEawrJC/mpileup.cram.urllist 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: @@ -3697,199 +3731,191 @@ .. 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 + /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 -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 + /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/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 + /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 -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' + /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 -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 + /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 -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 + /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/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 + /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/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 + /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/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 + /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/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 + /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 -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 + /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 -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 + /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/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 + /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 -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 + /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 -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 + /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 -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 + /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/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 + /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 -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 + /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/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 + /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/bcftools-1.9/test/csq/ENSG00000173376/ENSG00000173376.gff /build/bcftools-1.9/test/csq/ENSG00000173376/synon.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' +Parsing /build/bcftools-1.9/test/csq/ENSG00000173376/ENSG00000173376.gff ... +Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs Calling... .. ok test_csq_real: - /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/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 + /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... -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/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 + /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000375992/ENST00000375992.fa -g /build/bcftools-1.9/test/csq/ENST00000375992/ENST00000375992.gff /build/bcftools-1.9/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' +Parsing /build/bcftools-1.9/test/csq/ENST00000375992/ENST00000375992.gff ... +Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: - /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.9/test/csq/ENST00000218032/start-lost.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' + /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 -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' + /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 -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' + /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/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 + /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/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 + /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/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 + /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 @@ -3922,44 +3948,51 @@ .. 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 + /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 -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 + /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 -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 + /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/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 + /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 -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 + /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/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 + /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000382647/ENST00000382647.fa -g /build/bcftools-1.9/test/csq/ENST00000382647/ENST00000382647.gff /build/bcftools-1.9/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' +Parsing /build/bcftools-1.9/test/csq/ENST00000382647/ENST00000382647.gff ... +Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs +Calling... +.. ok + +test_csq_real: + /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000624631/ENST00000624631.fa -g /build/bcftools-1.9/test/csq/ENST00000624631/ENST00000624631.gff /build/bcftools-1.9/test/csq/ENST00000624631/ambiguous.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' +Parsing /build/bcftools-1.9/test/csq/ENST00000624631/ENST00000624631.gff ... +Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok @@ -3971,310 +4004,311 @@ .. 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 + /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/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 + /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/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 + /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/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 + /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/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 + /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/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 + /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 -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 + /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 -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 + /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 -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 + /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 -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 + /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 -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 + /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 -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 + /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 -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 + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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 + /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/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 + /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/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 + /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/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 + /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/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 + /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 -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 + /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/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 + /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/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 + /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 @@ -4291,7 +4325,7 @@ dh_testroot dh_prep dh_auto_install - make -j3 install DESTDIR=/build/bcftools-1.9/debian/bcftools AM_UPDATE_INFO_DIR=no + make -j4 install DESTDIR=/build/bcftools-1.9/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/bcftools-1.9' mkdir -p -m 755 /build/bcftools-1.9/debian/bcftools/usr/bin /build/bcftools-1.9/debian/bcftools/usr/share/man/man1 /build/bcftools-1.9/debian/bcftools/usr/lib/arm-linux-gnueabihf/bcftools install -p bcftools /build/bcftools-1.9/debian/bcftools/usr/bin @@ -4326,20 +4360,22 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.9-1_armhf.deb'. dpkg-deb: building package 'bcftools' in '../bcftools_1.9-1_armhf.deb'. +dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.9-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bcftools_1.9-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/14432/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14432/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/6149 and its subdirectories -I: Current time: Fri Jul 17 11:29:32 -12 2020 -I: pbuilder-time-stamp: 1595028572 +I: removing directory /srv/workspace/pbuilder/14432 and its subdirectories +I: Current time: Sat Jul 18 13:41:47 +14 2020 +I: pbuilder-time-stamp: 1595029307