Mon Nov 29 05:10:54 UTC 2021 I: starting to build bcftools/buster/amd64 on jenkins on '2021-11-29 05:10' Mon Nov 29 05:10:54 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_21/36597/console.log Mon Nov 29 05:10:54 UTC 2021 I: Downloading source for buster/bcftools=1.9-1 --2021-11-29 05:10:54-- http://deb.debian.org/debian/pool/main/b/bcftools/bcftools_1.9-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2093 (2.0K) Saving to: ‘bcftools_1.9-1.dsc’ 0K .. 100% 25.0M=0s 2021-11-29 05:10:54 (25.0 MB/s) - ‘bcftools_1.9-1.dsc’ saved [2093/2093] Mon Nov 29 05:10:54 UTC 2021 I: bcftools_1.9-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: bcftools Binary: bcftools Architecture: any Version: 1.9-1 Maintainer: Debian Med Packaging Team Uploaders: Afif Elghraoui Homepage: http://samtools.github.io/bcftools/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/bcftools Vcs-Git: https://salsa.debian.org/med-team/bcftools.git Testsuite: autopkgtest Testsuite-Triggers: perl, tabix Build-Depends: debhelper (>= 11~), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix , libio-pty-perl Package-List: bcftools deb science optional arch=any Checksums-Sha1: 9537a1746b4e434a85dd6ef21ffd5f6ef72f3c5f 2394968 bcftools_1.9.orig.tar.gz c36d2184ac4bcb31949d97fcb1412b0d4bc18017 6072 bcftools_1.9-1.debian.tar.xz Checksums-Sha256: 223b90c9a9b11576174384de70abe8e8394aef1b45c7324e4bf875d0f344e96e 2394968 bcftools_1.9.orig.tar.gz 0ed47d452a8997de10e6b6c711fcbeeb7aeea2e273d85eb1cce9efc3ee944677 6072 bcftools_1.9-1.debian.tar.xz Files: 9fdf519ebd35c70d44ed9b153b91f77a 2394968 bcftools_1.9.orig.tar.gz 3b24554ba588af6bd56e2b3dc1102d66 6072 bcftools_1.9-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAluOmwARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHb5A/+N7ieUYe5M23HKXcEzb+KXx57okB5ay69 0aWVws+1qW1VOjDmeYghJbBobjL6CBUjwM3DNEKcv2uUluxUH3V4GZfeIXLpASLH bEPNQtf00d7PHmBLCeGfCIoc+yIMggwgqH8ieo1PqXJiFW20nD95pnxVKnMB/hML YUcri3C0gmv54ndGP512CaXFSNbgegPHwzOFNPzbPq3XrcBbdR87yc6OY2V4KIBO b1FisxiG+zqJ1uKX64/2HaqejpFbklE1ZY0Wnij0AZDeG7uLrCbjCafmnGCNoRf8 ewZSqjiagySZJZnPus8J9aub7NLxZna+zv16rgZRiwiSgCmLRWSMvBcFdBsvGeih vOa8mTH2S68p58qbgABkvuearMUyZccXxtVRX26mritu7RZHzf/x/sZtgQC+MOut +6RJBuuChaLr0xC0KX4VFSVm3DZGwiOfsOy+PzwV7EFWRtwcg3T+kV9GwlTuyxR5 uTtiVfF/vMGgtiqhOLgySM3VVgqxIwSFgyunA6ZiMcZNNYBexkiPC47yMpn87VR1 wKYuFW0Nnx2tNEv0SjjYdkxCqLp8PgNlSUWgfzFcb3b9CSZ3afjr3giAavBM4Tbm A+1MR9OGwQeE5TYhxI8YrzRACpLusxWvC7VCbKWEtIs5wV5+VGZg3WjZx+8bVJke q8v1q2zlX+k= =IreV -----END PGP SIGNATURE----- Mon Nov 29 05:10:54 UTC 2021 I: Checking whether the package is not for us Mon Nov 29 05:10:54 UTC 2021 I: Starting 1st build on remote node ionos11-amd64.debian.net. Mon Nov 29 05:10:54 UTC 2021 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Mon Nov 29 05:12:14 UTC 2021 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 28 17:10:55 -12 2021 I: pbuilder-time-stamp: 1638162655 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bcftools_1.9-1.dsc] I: copying [./bcftools_1.9.orig.tar.gz] I: copying [./bcftools_1.9-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Sep 4 02:47:28 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcftools_1.9-1.dsc dpkg-source: info: extracting bcftools in bcftools-1.9 dpkg-source: info: unpacking bcftools_1.9.orig.tar.gz dpkg-source: info: unpacking bcftools_1.9-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying skip_new_test_failing_on_32bit.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2774139/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d8d7699ed4b74a24bea571932ca0a0f3' 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='2774139' PS1='# ' PS2='> ' 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.cDBzYlCgoz/pbuilderrc_AUqP --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.cDBzYlCgoz/b1 --logfile b1/build.log bcftools_1.9-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 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 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 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 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 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 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 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 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 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 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Nov 7 09:58 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 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/2774139/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.5-3), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.5-3); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on libio-pty-perl; however: Package libio-pty-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libbz2-dev{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu63{a} libio-pty-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 59 newly installed, 0 to remove and 0 not upgraded. Need to get 30.0 MB of archives. After unpacking 96.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libbz2-dev amd64 1.0.6-9.2~deb10u1 [30.2 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libgslcblas0 amd64 2.5+dfsg-6 [101 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libgsl23 amd64 2.5+dfsg-6 [880 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libgsl-dev amd64 2.5+dfsg-6 [1063 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 liblzma-dev amd64 5.2.4-1 [210 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libhts-dev amd64 1.9-12~deb10u1 [4347 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 tabix amd64 1.9-12~deb10u1 [292 kB] Fetched 30.0 MB in 4s (7857 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../22-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../25-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+deb10u2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../27-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../28-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../33-libbz2-dev_1.0.6-9.2~deb10u1_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.6-9.2~deb10u1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../34-libkeyutils1_1.6-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../35-libkrb5support0_1.17-3+deb10u3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../36-libk5crypto3_1.17-3+deb10u3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../37-libssl1.1_1.1.1d-0+deb10u7_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../38-libkrb5-3_1.17-3+deb10u3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../39-libgssapi-krb5-2_1.17-3+deb10u3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../40-libsasl2-modules-db_2.1.27+dfsg-1+deb10u1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../41-libsasl2-2_2.1.27+dfsg-1+deb10u1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../42-libldap-common_2.4.47+dfsg-3+deb10u6_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../43-libldap-2.4-2_2.4.47+dfsg-3+deb10u6_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../44-libnghttp2-14_1.36.0-2+deb10u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../45-libpsl5_0.20.2-2_amd64.deb ... Unpacking libpsl5:amd64 (0.20.2-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../46-librtmp1_2.4+20151223.gitfa8646d.1-2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../47-libssh2-1_1.8.0-2.1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../48-libcurl3-gnutls_7.64.0-4+deb10u2_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../49-libdeflate0_1.2-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.2-1) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../50-libgslcblas0_2.5+dfsg-6_amd64.deb ... Unpacking libgslcblas0:amd64 (2.5+dfsg-6) ... Selecting previously unselected package libgsl23:amd64. Preparing to unpack .../51-libgsl23_2.5+dfsg-6_amd64.deb ... Unpacking libgsl23:amd64 (2.5+dfsg-6) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../52-libgsl-dev_2.5+dfsg-6_amd64.deb ... Unpacking libgsl-dev (2.5+dfsg-6) ... Selecting previously unselected package libhts2:amd64. Preparing to unpack .../53-libhts2_1.9-12~deb10u1_amd64.deb ... Unpacking libhts2:amd64 (1.9-12~deb10u1) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../54-liblzma-dev_5.2.4-1_amd64.deb ... Unpacking liblzma-dev:amd64 (5.2.4-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../55-zlib1g-dev_1%3a1.2.11.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../56-libhts-dev_1.9-12~deb10u1_amd64.deb ... Unpacking libhts-dev:amd64 (1.9-12~deb10u1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../57-libio-pty-perl_1%3a1.08-1.1+b5_amd64.deb ... Unpacking libio-pty-perl (1:1.08-1.1+b5) ... Selecting previously unselected package tabix. Preparing to unpack .../58-tabix_1.9-12~deb10u1_amd64.deb ... Unpacking tabix (1.9-12~deb10u1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up libgslcblas0:amd64 (2.5+dfsg-6) ... Setting up libio-pty-perl (1:1.08-1.1+b5) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libgsl23:amd64 (2.5+dfsg-6) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up liblzma-dev:amd64 (5.2.4-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up libbz2-dev:amd64 (1.0.6-9.2~deb10u1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libgsl-dev (2.5+dfsg-6) ... Setting up libtool (2.4.6-9) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up tabix (1.9-12~deb10u1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:amd64 (1.9-12~deb10u1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package 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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bcftools_1.9-1_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.9-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean rm -f config.mk && touch config.mk dh clean dh_auto_clean make -j15 distclean make[1]: Entering directory '/build/bcftools-1.9' rm -f test/*.o test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f gmon.out *.o *~ bcftools version.h plugins/*.so plugins/*.P rm -rf *.dSYM plugins/*.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[1]: Leaving directory '/build/bcftools-1.9' dh_clean debian/rules build dh build dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/bcftools-1.9' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level make[1]: Leaving directory '/build/bcftools-1.9' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bcftools-1.9' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -ldl checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/bcftools-1.9' dh_auto_build make -j15 make[1]: Entering directory '/build/bcftools-1.9' echo '#define BCFTOOLS_VERSION "1.9"' > version.h gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/x86_64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split.so version.c plugins/split.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -ldl -ldl gcc -rdynamic -pthread -Wl,-z,relro -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o ccall.o em.o prob1.o kmin.o -lhts -lm -lz -ldl -ldl make[1]: Leaving directory '/build/bcftools-1.9' dh_auto_test make -j15 test VERBOSE=1 make[1]: Entering directory '/build/bcftools-1.9' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix= test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/yI1v9tGbwe/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-1.9/bcftools view -H /tmp/yI1v9tGbwe/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/yI1v9tGbwe/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-1.9/bcftools view -H /tmp/yI1v9tGbwe/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/yI1v9tGbwe/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/yI1v9tGbwe/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/yI1v9tGbwe/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/yI1v9tGbwe/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/yI1v9tGbwe/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/yI1v9tGbwe/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/yI1v9tGbwe/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/yI1v9tGbwe/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/yI1v9tGbwe/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.9/bcftools view -H /tmp/yI1v9tGbwe/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/yI1v9tGbwe/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/yI1v9tGbwe/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/yI1v9tGbwe/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/yI1v9tGbwe/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/yI1v9tGbwe/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/yI1v9tGbwe/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/yI1v9tGbwe/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/yI1v9tGbwe/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -s /tmp/yI1v9tGbwe/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/yI1v9tGbwe/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/yI1v9tGbwe/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.9/bcftools index -n /tmp/yI1v9tGbwe/empty.bcf .. ok test_vcf_check: /build/bcftools-1.9/bcftools stats -s - /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/check.1.chk /tmp/yI1v9tGbwe/check.2.chk /tmp/yI1v9tGbwe/check.3.chk /tmp/yI1v9tGbwe/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/yI1v9tGbwe/stats.a.vcf.gz /tmp/yI1v9tGbwe/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.9/bcftools stats -s B /tmp/yI1v9tGbwe/stats.a.vcf.gz /tmp/yI1v9tGbwe/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.9/bcftools stats -s - /tmp/yI1v9tGbwe/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -n =2 /tmp/yI1v9tGbwe/isec.a.vcf.gz /tmp/yI1v9tGbwe/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -Ob -n =2 /tmp/yI1v9tGbwe/isec.a.vcf.gz /tmp/yI1v9tGbwe/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/yI1v9tGbwe/isec.a.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/isec.a.vcf.gz /tmp/yI1v9tGbwe/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -n =2 -c both /tmp/yI1v9tGbwe/isec.a.vcf.gz /tmp/yI1v9tGbwe/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -Ob -n =2 -c both /tmp/yI1v9tGbwe/isec.a.vcf.gz /tmp/yI1v9tGbwe/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -n =2 -c any /tmp/yI1v9tGbwe/isec.a.vcf.gz /tmp/yI1v9tGbwe/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -Ob -n =2 -c any /tmp/yI1v9tGbwe/isec.a.vcf.gz /tmp/yI1v9tGbwe/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -C -c any /tmp/yI1v9tGbwe/isec.a.vcf.gz /tmp/yI1v9tGbwe/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /build/bcftools-1.9/bcftools isec -Ob -C -c any /tmp/yI1v9tGbwe/isec.a.vcf.gz /tmp/yI1v9tGbwe/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /build/bcftools-1.9/bcftools isec --no-version -T /tmp/yI1v9tGbwe/isec.tab.gz /tmp/yI1v9tGbwe/isec.a.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /build/bcftools-1.9/bcftools isec -Ob -T /tmp/yI1v9tGbwe/isec.tab.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/merge.a.vcf.gz /tmp/yI1v9tGbwe/merge.b.vcf.gz /tmp/yI1v9tGbwe/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples /tmp/yI1v9tGbwe/merge.a.vcf.gz /tmp/yI1v9tGbwe/merge.b.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/merge.a.vcf.gz /tmp/yI1v9tGbwe/merge.b.vcf.gz /tmp/yI1v9tGbwe/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -Fx /tmp/yI1v9tGbwe/merge.a.vcf.gz /tmp/yI1v9tGbwe/merge.b.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/merge.a.vcf.gz /tmp/yI1v9tGbwe/merge.b.vcf.gz /tmp/yI1v9tGbwe/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -0 /tmp/yI1v9tGbwe/merge.a.vcf.gz /tmp/yI1v9tGbwe/merge.b.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/merge.2.a.vcf.gz /tmp/yI1v9tGbwe/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -m none /tmp/yI1v9tGbwe/merge.2.a.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/merge.2.a.vcf.gz /tmp/yI1v9tGbwe/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -m both /tmp/yI1v9tGbwe/merge.2.a.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/merge.2.a.vcf.gz /tmp/yI1v9tGbwe/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -m all /tmp/yI1v9tGbwe/merge.2.a.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/merge.3.a.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/merge.3.a.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/merge.4.a.vcf.gz /tmp/yI1v9tGbwe/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --force-samples -m id /tmp/yI1v9tGbwe/merge.4.a.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/gvcf.merge.1.vcf.gz /tmp/yI1v9tGbwe/gvcf.merge.2.vcf.gz /tmp/yI1v9tGbwe/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/yI1v9tGbwe/gvcf.merge.1.vcf.gz /tmp/yI1v9tGbwe/gvcf.merge.2.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/merge.gvcf.2.a.vcf.gz /tmp/yI1v9tGbwe/merge.gvcf.2.b.vcf.gz /tmp/yI1v9tGbwe/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/yI1v9tGbwe/merge.gvcf.2.a.vcf.gz /tmp/yI1v9tGbwe/merge.gvcf.2.b.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/merge.gvcf.3.a.vcf.gz /tmp/yI1v9tGbwe/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob --gvcf - -i SRC:join /tmp/yI1v9tGbwe/merge.gvcf.3.a.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/merge.5.a.vcf.gz /tmp/yI1v9tGbwe/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.9/bcftools merge -Ob /tmp/yI1v9tGbwe/merge.5.a.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m- /tmp/yI1v9tGbwe/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/yI1v9tGbwe/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m- /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/yI1v9tGbwe/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/yI1v9tGbwe/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/yI1v9tGbwe/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/yI1v9tGbwe/norm.merge.3.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m+ /tmp/yI1v9tGbwe/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/yI1v9tGbwe/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -m+ -s /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d snps /tmp/yI1v9tGbwe/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/yI1v9tGbwe/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d indels /tmp/yI1v9tGbwe/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/yI1v9tGbwe/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d both /tmp/yI1v9tGbwe/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/yI1v9tGbwe/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d all /tmp/yI1v9tGbwe/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/yI1v9tGbwe/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /build/bcftools-1.9/bcftools norm -Ob -d none /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -f PASS -Xks NA00003 /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -xs NA00003 /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -p /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -P /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -GVsnps /tmp/yI1v9tGbwe/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -GVsnps /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -s ^NA00003 /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -G /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -a /tmp/yI1v9tGbwe/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -a /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -asA /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -asB /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -asA /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/yI1v9tGbwe/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i'TXT0="text"' /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-1.9/bcftools view -Ob -i 'POS>=3062917' /tmp/yI1v9tGbwe/filter.2.vcf.gz 1:3062917-3157410 | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S. -e'TXT0="text"' /build/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S. -e'TXT0="text"' /build/bcftools-1.9/test/view.filter.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-1.9/test/view.filter.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-1.9/test/view.filter.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-1.9/test/view.filter.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-1.9/test/view.filter.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S. -e'FMT/STR="XX"' /build/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/bcftools-1.9/test/view.filter.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -C5:nonmajor /tmp/yI1v9tGbwe/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -c6:nonmajor /tmp/yI1v9tGbwe/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -q0.3:major /tmp/yI1v9tGbwe/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/yI1v9tGbwe/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/yI1v9tGbwe/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.9/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/yI1v9tGbwe/view.filter.annovar.vcf.gz .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -mv /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -mv /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -mg0 /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -mg0 /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.samples /build/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.samples /build/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.ped /build/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.ped /build/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.2.samples /build/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.2.samples /build/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.9/bcftools call --no-version -mA -C alleles -T /tmp/yI1v9tGbwe/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/yI1v9tGbwe/mpileup.tab.gz /build/bcftools-1.9/test/mpileup.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -cv /build/bcftools-1.9/test/mpileup.c.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -cv /build/bcftools-1.9/test/mpileup.c.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.samples /build/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.samples /build/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.ped /build/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.ped /build/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.9/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.2.samples /build/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /build/bcftools-1.9/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.9/test/mpileup.ploidy -S /build/bcftools-1.9/test/mpileup.2.samples /build/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -mx -g2 -G2 /build/bcftools-1.9/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -mx -g2 -G2 /build/bcftools-1.9/test/filter.1.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-1.9/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'INFO/DP=19' /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'INFO/DP=19' -s XX /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'INFO/DP=19' -s XX -mx /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' -s XX /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-1.9/test/filter.3.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'ALT="."' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'ALT="."' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/bcftools-1.9/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/bcftools-1.9/test/filter.4.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/bcftools-1.9/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/bcftools-1.9/test/filter.4.vcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="A"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="A"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="RR"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="RR"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="RA"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="RA"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="AR"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="AR"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="AA"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="AA"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="aA"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="aA"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="Aa"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="Aa"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="HOM"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="HOM"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="HET"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="HET"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'GT="HAP"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'GT="HAP"' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'AD[:1]=11' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'AD[:1]=11' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'AD[1:]=11' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'AD[1:]=11' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'FR[0:1]=11' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'FR[0:1]=11' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'AD[*]="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'AD[*]="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'AD[0:0]=="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'AD[0:0]=="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'AD[0:0]!="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'AD[0:0]!="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'QUAL=="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'QUAL=="."' /build/bcftools-1.9/test/filter.5.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'N_PASS(DP>32)=1' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -i'F_PASS(DP>32)=0.5' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.9/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/bcftools-1.9/test/filter.2.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_sort: /build/bcftools-1.9/bcftools sort -m 0 /build/bcftools-1.9/test/sort.vcf | /build/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.9exMW2 Merging 17 temporary files Cleaning Done .. ok test_vcf_sort: /build/bcftools-1.9/bcftools sort -Ob -m 0 /build/bcftools-1.9/test/sort.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.2L7OJ1 Merging 17 temporary files Cleaning Done .. ok test_vcf_sort: /build/bcftools-1.9/bcftools sort -m 1000 /build/bcftools-1.9/test/sort.vcf | /build/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.fdEN94 Merging 5 temporary files Cleaning Done .. ok test_vcf_sort: /build/bcftools-1.9/bcftools sort -Ob -m 1000 /build/bcftools-1.9/test/sort.vcf | /build/bcftools-1.9/bcftools view | /build/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.koPvY3 Merging 5 temporary files Cleaning Done .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.9/test/regions.tab /tmp/yI1v9tGbwe/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/yI1v9tGbwe/regions.tab.gz /tmp/yI1v9tGbwe/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/yI1v9tGbwe/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/yI1v9tGbwe/regions.tab.gz /tmp/yI1v9tGbwe/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/yI1v9tGbwe/regions.bed /tmp/yI1v9tGbwe/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/yI1v9tGbwe/regions.bed .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/yI1v9tGbwe/regions.bed /tmp/yI1v9tGbwe/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/yI1v9tGbwe/regions.bed.gz /tmp/yI1v9tGbwe/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/regions.vcf.gz | /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/yI1v9tGbwe/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/yI1v9tGbwe/regions.bed.gz /tmp/yI1v9tGbwe/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/yI1v9tGbwe/annotate2.vcf.gz 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-1.9/test/annotate3.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-1.9/test/annotate3.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -x FORMAT /build/bcftools-1.9/test/annotate3.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -Ob -x FORMAT /build/bcftools-1.9/test/annotate3.vcf 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.9/bcftools annotate -a /tmp/yI1v9tGbwe/annots4.vcf.gz -c +INFO /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots4.vcf.gz -c +INFO /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots11.vcf.gz -c FMT /tmp/yI1v9tGbwe/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/yI1v9tGbwe/annots11.vcf.gz -c FMT /tmp/yI1v9tGbwe/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/yI1v9tGbwe/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +missing2ref --no-version /tmp/yI1v9tGbwe/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +setGT --no-version /tmp/yI1v9tGbwe/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/yI1v9tGbwe/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +setGT --no-version /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-AN-AC --no-version /tmp/yI1v9tGbwe/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +dosage /tmp/yI1v9tGbwe/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +dosage /tmp/yI1v9tGbwe/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixploidy --no-version /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fill-tags --no-version /tmp/yI1v9tGbwe/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/yI1v9tGbwe/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTisec /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixref /tmp/yI1v9tGbwe/fixref.2a.vcf.gz -- -f /build/bcftools-1.9/test/norm.fa -i /tmp/yI1v9tGbwe/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixref /tmp/yI1v9tGbwe/fixref.2a.bcf -- -f /build/bcftools-1.9/test/norm.fa -i /tmp/yI1v9tGbwe/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +fixref /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/yI1v9tGbwe/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +GTsubset --no-version /tmp/yI1v9tGbwe/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/yI1v9tGbwe/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +mendelian /tmp/yI1v9tGbwe/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/yI1v9tGbwe/mendelian.bcf -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +mendelian /tmp/yI1v9tGbwe/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/yI1v9tGbwe/mendelian.bcf -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +mendelian /tmp/yI1v9tGbwe/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/yI1v9tGbwe/mendelian.bcf -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /build/bcftools-1.9/bcftools +contrast /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/concat.1.a.vcf.gz /tmp/yI1v9tGbwe/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob /tmp/yI1v9tGbwe/concat.1.a.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/concat.1.a.bcf /tmp/yI1v9tGbwe/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob /tmp/yI1v9tGbwe/concat.1.a.bcf /tmp/yI1v9tGbwe/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/yI1v9tGbwe/concat.2.a.vcf.gz /tmp/yI1v9tGbwe/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -a /tmp/yI1v9tGbwe/concat.2.a.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/concat.2.a.bcf /tmp/yI1v9tGbwe/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -a /tmp/yI1v9tGbwe/concat.2.a.bcf /tmp/yI1v9tGbwe/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/yI1v9tGbwe/concat.2.a.vcf.gz /tmp/yI1v9tGbwe/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -aD /tmp/yI1v9tGbwe/concat.2.a.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/concat.2.a.bcf /tmp/yI1v9tGbwe/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -aD /tmp/yI1v9tGbwe/concat.2.a.bcf /tmp/yI1v9tGbwe/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/yI1v9tGbwe/concat.3.a.vcf.gz /tmp/yI1v9tGbwe/concat.3.b.vcf.gz /tmp/yI1v9tGbwe/concat.3.0.vcf.gz /tmp/yI1v9tGbwe/concat.3.c.vcf.gz /tmp/yI1v9tGbwe/concat.3.d.vcf.gz /tmp/yI1v9tGbwe/concat.3.e.vcf.gz /tmp/yI1v9tGbwe/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -l /tmp/yI1v9tGbwe/concat.3.a.vcf.gz /tmp/yI1v9tGbwe/concat.3.b.vcf.gz /tmp/yI1v9tGbwe/concat.3.0.vcf.gz /tmp/yI1v9tGbwe/concat.3.c.vcf.gz /tmp/yI1v9tGbwe/concat.3.d.vcf.gz /tmp/yI1v9tGbwe/concat.3.e.vcf.gz /tmp/yI1v9tGbwe/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/yI1v9tGbwe/concat.3.a.bcf /tmp/yI1v9tGbwe/concat.3.b.bcf /tmp/yI1v9tGbwe/concat.3.0.bcf /tmp/yI1v9tGbwe/concat.3.c.bcf /tmp/yI1v9tGbwe/concat.3.d.bcf /tmp/yI1v9tGbwe/concat.3.e.bcf /tmp/yI1v9tGbwe/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-1.9/bcftools concat -Ob -l /tmp/yI1v9tGbwe/concat.3.a.bcf /tmp/yI1v9tGbwe/concat.3.b.bcf /tmp/yI1v9tGbwe/concat.3.0.bcf /tmp/yI1v9tGbwe/concat.3.c.bcf /tmp/yI1v9tGbwe/concat.3.d.bcf /tmp/yI1v9tGbwe/concat.3.e.bcf /tmp/yI1v9tGbwe/concat.3.f.bcf | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 950847362 .. ok test_naive_concat: /build/bcftools-1.9/bcftools concat --naive /tmp/yI1v9tGbwe/naive_concat.0.bcf /tmp/yI1v9tGbwe/naive_concat.1.bcf /tmp/yI1v9tGbwe/naive_concat.2.bcf /tmp/yI1v9tGbwe/naive_concat.3.bcf /tmp/yI1v9tGbwe/naive_concat.4.bcf /tmp/yI1v9tGbwe/naive_concat.5.bcf /tmp/yI1v9tGbwe/naive_concat.6.bcf /tmp/yI1v9tGbwe/naive_concat.7.bcf /tmp/yI1v9tGbwe/naive_concat.8.bcf /tmp/yI1v9tGbwe/naive_concat.9.bcf | /build/bcftools-1.9/bcftools view -H .. ok test_naive_concat: /build/bcftools-1.9/bcftools concat --naive /tmp/yI1v9tGbwe/naive_concat.0.vcf.gz /tmp/yI1v9tGbwe/naive_concat.1.vcf.gz /tmp/yI1v9tGbwe/naive_concat.2.vcf.gz /tmp/yI1v9tGbwe/naive_concat.3.vcf.gz /tmp/yI1v9tGbwe/naive_concat.4.vcf.gz /tmp/yI1v9tGbwe/naive_concat.5.vcf.gz /tmp/yI1v9tGbwe/naive_concat.6.vcf.gz /tmp/yI1v9tGbwe/naive_concat.7.vcf.gz /tmp/yI1v9tGbwe/naive_concat.8.vcf.gz /tmp/yI1v9tGbwe/naive_concat.9.vcf.gz | /build/bcftools-1.9/bcftools view -H .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr /tmp/yI1v9tGbwe/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/yI1v9tGbwe/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/yI1v9tGbwe/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/yI1v9tGbwe/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.hdr | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples /tmp/yI1v9tGbwe/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/yI1v9tGbwe/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/yI1v9tGbwe/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/yI1v9tGbwe/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 /tmp/yI1v9tGbwe/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/yI1v9tGbwe/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/yI1v9tGbwe/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/yI1v9tGbwe/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples2 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 /tmp/yI1v9tGbwe/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/yI1v9tGbwe/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/yI1v9tGbwe/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/yI1v9tGbwe/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples3 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.9/test/reheader.vcf | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 /tmp/yI1v9tGbwe/reheader.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/yI1v9tGbwe/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/yI1v9tGbwe/reheader.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/yI1v9tGbwe/reheader.vcf.gz | /build/bcftools-1.9/bcftools reheader -s /build/bcftools-1.9/test/reheader.samples4 | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr /build/bcftools-1.9/test/empty.vcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.9/test/empty.vcf | /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.9/bcftools reheader -h /build/bcftools-1.9/test/reheader.empty.hdr /tmp/yI1v9tGbwe/empty.bcf | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/yI1v9tGbwe/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/yI1v9tGbwe/empty.vcf.gz | /build/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/yI1v9tGbwe/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/yI1v9tGbwe/rename.map -Ov /tmp/yI1v9tGbwe/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/yI1v9tGbwe/rename.map -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/convert.vcf.gz | /build/bcftools-1.9/bcftools convert -h .,.,- 2>/dev/null .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.9/bcftools convert -H /build/bcftools-1.9/test/convert.hls.gt.hap,/build/bcftools-1.9/test/convert.hls.gt.legend,/build/bcftools-1.9/test/convert.hls.gt.samples 2>/dev/null | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.9/bcftools convert -H /build/bcftools-1.9/test/convert.hls.gt.hap,/build/bcftools-1.9/test/convert.hls.gt.legend,/build/bcftools-1.9/test/convert.hls.gt.samples -Ou 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.9/bcftools convert --hapsample2vcf /build/bcftools-1.9/test/convert.hs.gt.hap,/build/bcftools-1.9/test/convert.hs.gt.samples 2>/dev/null | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.9/bcftools convert --hapsample2vcf /build/bcftools-1.9/test/convert.hs.gt.hap,/build/bcftools-1.9/test/convert.hs.gt.samples -Ou 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-1.9/bcftools convert --hapsample -,. /tmp/yI1v9tGbwe/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/convert.hap-missing.vcf.gz 2>/dev/null .. ok test_vcf_convert: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/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/yI1v9tGbwe/convert.gvcf.vcf.gz 2>/dev/null .. ok test_vcf_convert_gvcf: /build/bcftools-1.9/bcftools view -Ob /tmp/yI1v9tGbwe/convert.gvcf.vcf.gz | /build/bcftools-1.9/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.9/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/bcftools-1.9/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-1.9/test/23andme.fa --tsv2vcf /build/bcftools-1.9/test/convert.23andme 2>/dev/null .. ok test_vcf_convert_tsv2vcf: /build/bcftools-1.9/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-1.9/test/23andme.fa --tsv2vcf /build/bcftools-1.9/test/convert.23andme 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/yI1v9tGbwe/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/yI1v9tGbwe/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -m /build/bcftools-1.9/test/consensus.tab -c /tmp/yI1v9tGbwe/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/yI1v9tGbwe/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/yI1v9tGbwe/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/yI1v9tGbwe/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 -m /build/bcftools-1.9/test/consensus.tab -c /tmp/yI1v9tGbwe/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/yI1v9tGbwe/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/yI1v9tGbwe/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/yI1v9tGbwe/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -I -m /build/bcftools-1.9/test/consensus.tab -c /tmp/yI1v9tGbwe/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/yI1v9tGbwe/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/yI1v9tGbwe/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/yI1v9tGbwe/consensus.vcf.gz -f /build/bcftools-1.9/test/consensus.fa -H 1 -c /tmp/yI1v9tGbwe/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/yI1v9tGbwe/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-1.9/bcftools consensus /tmp/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/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/yI1v9tGbwe/consensus3.vcf.gz -f /build/bcftools-1.9/test/consensus2.fa -H 2 -M "?" 2>/dev/null .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -b /tmp/yI1v9tGbwe/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/yI1v9tGbwe/mpileup.bam.urllist 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -b /tmp/yI1v9tGbwe/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/yI1v9tGbwe/mpileup.cram.urllist 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S /build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S /build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S /build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S /build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.9/test/mplp.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -S /build/bcftools-1.9/test/mplp.9.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -S /build/bcftools-1.9/test/mplp.9.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -S /build/bcftools-1.9/test/mplp.9.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -S /build/bcftools-1.9/test/mplp.9.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -G /build/bcftools-1.9/test/mplp.10.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -G /build/bcftools-1.9/test/mplp.10.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.bam /build/bcftools-1.9/test/mpileup/mpileup.2.bam /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -G /build/bcftools-1.9/test/mplp.10.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -t17:100-150 -G /build/bcftools-1.9/test/mplp.10.samples -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.1.cram /build/bcftools-1.9/test/mpileup/mpileup.2.cram /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s HG00102 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.bam /build/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -G /build/bcftools-1.9/test/mplp.11.rgs -f /build/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.9/test/mpileup/mpileup.3.cram /build/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a AD -f /build/bcftools-1.9/test/mpileup/indel-AD.1.fa /build/bcftools-1.9/test/mpileup/indel-AD.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a AD -f /build/bcftools-1.9/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.9/test/mpileup/indel-AD.1.bam 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a AD -f /build/bcftools-1.9/test/mpileup/indel-AD.1.fa /build/bcftools-1.9/test/mpileup/indel-AD.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.9/bcftools mpileup -a AD -f /build/bcftools-1.9/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.9/test/mpileup/indel-AD.1.cram 2>/dev/null | /build/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq.fa -g /build/bcftools-1.9/test/csq.gff3 /build/bcftools-1.9/test/csq.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq.gff3 ... Indexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000624631/ENST00000624631.fa -g /build/bcftools-1.9/test/csq/ENST00000624631/ENST00000624631.gff /build/bcftools-1.9/test/csq/ENST00000624631/ambiguous.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000624631/ENST00000624631.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000593942/ENST00000593942.fa -g /build/bcftools-1.9/test/csq/ENST00000593942/ENST00000593942.gff /build/bcftools-1.9/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000593942/ENST00000593942.gff ... Indexed 1 transcripts, 7 exons, 4 CDSs, 5 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.9/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.gff ... Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.9/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.gff ... Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000557788/ENST00000557788.fa -g /build/bcftools-1.9/test/csq/ENST00000557788/ENST00000557788.gff /build/bcftools-1.9/test/csq/ENST00000557788/long-overlap-del.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000557788/ENST00000557788.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000545279/ENST00000545279.fa -g /build/bcftools-1.9/test/csq/ENST00000545279/ENST00000545279.gff /build/bcftools-1.9/test/csq/ENST00000545279/splice-region-insert.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000545279/ENST00000545279.gff ... Indexed 1 transcripts, 9 exons, 7 CDSs, 4 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.9/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.9/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.9/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.gff ... Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.9/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.gff ... Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.9/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.9/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000528237/ENST00000528237.fa -g /build/bcftools-1.9/test/csq/ENST00000528237/ENST00000528237.gff /build/bcftools-1.9/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000528237/ENST00000528237.gff ... Indexed 1 transcripts, 7 exons, 6 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000520868/ENST00000520868.fa -g /build/bcftools-1.9/test/csq/ENST00000520868/ENST00000520868.gff /build/bcftools-1.9/test/csq/ENST00000520868/long-deletion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000520868/ENST00000520868.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.9/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.9/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000519442/ENST00000519442.fa -g /build/bcftools-1.9/test/csq/ENST00000519442/ENST00000519442.gff /build/bcftools-1.9/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000519442/ENST00000519442.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.9/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.gff ... Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.9/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.gff ... Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000448695/ENST00000448695.fa -g /build/bcftools-1.9/test/csq/ENST00000448695/ENST00000448695.gff /build/bcftools-1.9/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000448695/ENST00000448695.gff ... Indexed 1 transcripts, 26 exons, 26 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000436063/ENST00000436063.fa -g /build/bcftools-1.9/test/csq/ENST00000436063/ENST00000436063.gff /build/bcftools-1.9/test/csq/ENST00000436063/insert-before-utr.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000436063/ENST00000436063.gff ... Indexed 1 transcripts, 7 exons, 7 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.9/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.9/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.9/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.9/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-1.9/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-1.9/test/csq/ENST00000420670/start-stop-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000420670/ENST00000420670.gff ... Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000413103/ENST00000413103.fa -g /build/bcftools-1.9/test/csq/ENST00000413103/ENST00000413103.gff /build/bcftools-1.9/test/csq/ENST00000413103/long-deletion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000413103/ENST00000413103.gff ... Indexed 1 transcripts, 2 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000410009/ENST00000410009.fa -g /build/bcftools-1.9/test/csq/ENST00000410009/ENST00000410009.gff /build/bcftools-1.9/test/csq/ENST00000410009/frameshift.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000410009/ENST00000410009.gff ... Indexed 1 transcripts, 6 exons, 6 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000409523/ENST00000409523.fa -g /build/bcftools-1.9/test/csq/ENST00000409523/ENST00000409523.gff /build/bcftools-1.9/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000409523/ENST00000409523.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000390520/ENST00000390520.fa -g /build/bcftools-1.9/test/csq/ENST00000390520/ENST00000390520.gff /build/bcftools-1.9/test/csq/ENST00000390520/deletion-overlap.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000390520/ENST00000390520.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000382647/ENST00000382647.fa -g /build/bcftools-1.9/test/csq/ENST00000382647/ENST00000382647.gff /build/bcftools-1.9/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000382647/ENST00000382647.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000381157/ENST00000381157.fa -g /build/bcftools-1.9/test/csq/ENST00000381157/ENST00000381157.gff /build/bcftools-1.9/test/csq/ENST00000381157/haploid-diploid.vcf | /build/bcftools-1.9/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' Parsing /build/bcftools-1.9/test/csq/ENST00000381157/ENST00000381157.gff ... Indexed 1 transcripts, 6 exons, 6 CDSs, 0 UTRs Calling... Warning: Skipping site with non-diploid/non-haploid genotypes at X:31180 C>T .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.9/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.9/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000375992/ENST00000375992.fa -g /build/bcftools-1.9/test/csq/ENST00000375992/ENST00000375992.gff /build/bcftools-1.9/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000375992/ENST00000375992.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.9/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.gff ... Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.9/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.gff ... Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000368801/ENST00000368801.fa -g /build/bcftools-1.9/test/csq/ENST00000368801/ENST00000368801.gff /build/bcftools-1.9/test/csq/ENST00000368801/compound-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000368801/ENST00000368801.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000357367/ENST00000357367.fa -g /build/bcftools-1.9/test/csq/ENST00000357367/ENST00000357367.gff /build/bcftools-1.9/test/csq/ENST00000357367/stop-retained.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000357367/ENST00000357367.gff ... Indexed 1 transcripts, 4 exons, 3 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.9/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.9/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.9/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.9/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.gff ... Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.9/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.gff ... Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.9/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.9/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000301246/ENST00000301246.fa -g /build/bcftools-1.9/test/csq/ENST00000301246/ENST00000301246.gff /build/bcftools-1.9/test/csq/ENST00000301246/15bp-insert.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000301246/ENST00000301246.gff ... Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.9/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.gff ... Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.9/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.gff ... Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.9/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.9/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000271583/ENST00000271583.fa -g /build/bcftools-1.9/test/csq/ENST00000271583/ENST00000271583.gff /build/bcftools-1.9/test/csq/ENST00000271583/splice-acceptor.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000271583/ENST00000271583.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000256452/ENST00000256452.fa -g /build/bcftools-1.9/test/csq/ENST00000256452/ENST00000256452.gff /build/bcftools-1.9/test/csq/ENST00000256452/intron.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000256452/ENST00000256452.gff ... Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000227471/ENST00000227471.fa -g /build/bcftools-1.9/test/csq/ENST00000227471/ENST00000227471.gff /build/bcftools-1.9/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000227471/ENST00000227471.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.9/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -l -f /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.9/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.9/test/csq/ENST00000218032/start-lost-del.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /build/bcftools-1.9/bcftools csq -f /build/bcftools-1.9/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/bcftools-1.9/test/csq/ENSG00000173376/ENSG00000173376.gff /build/bcftools-1.9/test/csq/ENSG00000173376/synon.vcf | /build/bcftools-1.9/test/csq/sort-csq | /build/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /build/bcftools-1.9/test/csq/ENSG00000173376/ENSG00000173376.gff ... Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs Calling... .. ok Number of tests: total .. 821 passed .. 821 failed .. 0 make[1]: Leaving directory '/build/bcftools-1.9' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j15 install DESTDIR=/build/bcftools-1.9/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/bcftools-1.9' mkdir -p -m 755 /build/bcftools-1.9/debian/bcftools/usr/bin /build/bcftools-1.9/debian/bcftools/usr/share/man/man1 /build/bcftools-1.9/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /build/bcftools-1.9/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /build/bcftools-1.9/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/bcftools-1.9/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/bcftools-1.9/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools make[1]: Leaving directory '/build/bcftools-1.9' debian/rules override_dh_install make[1]: Entering directory '/build/bcftools-1.9' dh_install # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/build/bcftools-1.9' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/bcftools-1.9' dh_installman --language=C make[1]: Leaving directory '/build/bcftools-1.9' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools' in '../bcftools_1.9-1_amd64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.9-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bcftools_1.9-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: 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/2774139 and its subdirectories I: Current time: Sun Nov 28 17:12:14 -12 2021 I: pbuilder-time-stamp: 1638162734 Mon Nov 29 05:12:14 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Mon Nov 29 05:12:14 UTC 2021 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Mon Nov 29 05:14:27 UTC 2021 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Mon Nov 29 05:14:27 UTC 2021 I: bcftools_1.9-1_amd64.changes: Format: 1.8 Date: Tue, 04 Sep 2018 16:37:32 +0200 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: amd64 Version: 1.9-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Changes: bcftools (1.9-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.2.1 * Fix Perl interpreter PATH Checksums-Sha1: 72ae66ccc0de471144563d5bd79f433be1865f47 1720088 bcftools-dbgsym_1.9-1_amd64.deb aace7f6811b1696710254838641db933d1ac8e6e 5748 bcftools_1.9-1_amd64.buildinfo 244188c3138e6ad9474fce9c98933ea039d6a6a2 531384 bcftools_1.9-1_amd64.deb Checksums-Sha256: cff68de572b2047675352c09a8dbd65e3619223fb7b1e01c06313e021fb9f38a 1720088 bcftools-dbgsym_1.9-1_amd64.deb 35820c2d04ddc0075d6c02cabc5d4901bb23163fb4e7ef89783e1f66ce51772d 5748 bcftools_1.9-1_amd64.buildinfo c91a2626ed6cbbf778a3b1661da8e8786b02bcd4412ff578490fbed342aa1a06 531384 bcftools_1.9-1_amd64.deb Files: 81c14aa31ea6bf3ea0ab1cc43cd64efa 1720088 debug optional bcftools-dbgsym_1.9-1_amd64.deb 066922f37e4ecd4cb22b4784a9036fa2 5748 science optional bcftools_1.9-1_amd64.buildinfo 710d39e1063fc75f290a3af9ae7b7285 531384 science optional bcftools_1.9-1_amd64.deb Mon Nov 29 05:14:28 UTC 2021 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.cDBzYlCgoz/bcftools_1.9-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.cDBzYlCgoz/bcftools_1.9-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.cDBzYlCgoz/bcftools_1.9-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.cDBzYlCgoz/b1/bcftools_1.9-1_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.cDBzYlCgoz/b2/bcftools_1.9-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.248s) 0.248s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.043s) 0.043s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Mon Nov 29 05:14:29 UTC 2021 I: found no differences in the changes files, and a .buildinfo file also exists. Mon Nov 29 05:14:29 UTC 2021 I: bcftools from buster built successfully and reproducibly on amd64. Mon Nov 29 05:14:30 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Nov 29 05:14:30 UTC 2021 I: Submitting 8.0K b1/bcftools_1.9-1_amd64.buildinfo.asc Mon Nov 29 05:14:31 UTC 2021 I: Submitting 8.0K b2/bcftools_1.9-1_amd64.buildinfo.asc Mon Nov 29 05:14:32 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Nov 29 05:14:32 UTC 2021 I: Done submitting .buildinfo files. Mon Nov 29 05:14:32 UTC 2021 I: Removing signed bcftools_1.9-1_amd64.buildinfo.asc files: removed './b1/bcftools_1.9-1_amd64.buildinfo.asc' removed './b2/bcftools_1.9-1_amd64.buildinfo.asc'