Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/bcftools/bcftools_1.13-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/bcftools-1.13-154vetjdw/bcftools_1.13-1_amd64.buildinfo Get source package info: bcftools=1.13-1 Source URL: http://snapshot.notset.fr/mr/package/bcftools/1.13-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.4-1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.51 bash=5.1-3+b1 binutils=2.37-4 binutils-common=2.37-4 binutils-x86-64-linux-gnu=2.37-4 bsdextrautils=2.37.2-1 bsdutils=1:2.37.2-1 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.3.0-7 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.4.1 debianutils=5.4-3 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.3.0-7 gcc=4:10.2.1-1 gcc-10=10.3.0-7 gcc-10-base=10.3.0-7 gcc-11-base=11.2.0-3 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libasan6=11.2.0-3 libatomic1=11.2.0-3 libattr1=1:2.4.48-6 libaudit-common=1:3.0.5-1 libaudit1=1:3.0.5-1 libbinutils=2.37-4 libblkid1=2.37.2-1 libbrotli1=1.0.9-2+b2 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-17 libc-dev-bin=2.31-17 libc6=2.31-17 libc6-dev=2.31-17 libcap-ng0=0.7.9-2.2+b1 libcc1-0=11.2.0-3 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.25-1 libcrypt1=1:4.4.25-1 libctf-nobfd0=2.37-4 libctf0=2.37-4 libcurl3-gnutls=7.74.0-1.3+b1 libcurl4-gnutls-dev=7.74.0-1.3+b1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.4.1 libdeflate-dev=1.7-2 libdeflate0=1.7-2 libdpkg-perl=1.20.9 libelf1=0.185-2 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.12.0-1 libgcc-10-dev=10.3.0-7 libgcc-s1=11.2.0-3 libgcrypt20=1.8.7-6 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.2-2 libgomp1=11.2.0-3 libgpg-error0=1.42-3 libgsl-dev=2.7+dfsg-2 libgsl25=2.7+dfsg-2 libgslcblas0=2.7+dfsg-2 libgssapi-krb5-2=1.18.3-6 libhogweed6=3.7.3-1 libhts-dev=1.13+ds-1 libhts3=1.13+ds-1 libhtscodecs2=1.1.1-2 libicu67=67.1-7 libidn2-0=2.3.2-2 libio-pty-perl=1:1.15-2 libisl23=0.23-1 libitm1=11.2.0-3 libk5crypto3=1.18.3-6 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-6 libkrb5support0=1.18.3-6 libldap-2.4-2=2.4.57+dfsg-3 liblsan0=11.2.0-3 liblz4-1=1.9.3-2 liblzma-dev=5.2.5-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.37.2-1 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-9 libpam-modules-bin=1.4.0-9 libpam-runtime=1.4.0-9 libpam0g=1.4.0-9 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-5 libpipeline1=1.5.3-1 libpsl5=0.21.0-1.2 libquadmath0=11.2.0-3 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsmartcols1=2.37.2-1 libssh2-1=1.9.0-3 libssl1.1=1.1.1l-1 libstdc++-10-dev=10.3.0-7 libstdc++6=11.2.0-3 libsub-override-perl=0.09-2 libsystemd0=247.9-1 libtasn1-6=4.17.0-2 libtinfo6=6.2+20201114-4 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-3 libubsan1=11.2.0-3 libuchardet0=0.0.7-1 libudev1=247.9-1 libunistring2=0.9.10-6 libuuid1=2.37.2-1 libxml2=2.9.10+dfsg-6.7 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.46-4 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-4 ncurses-bin=6.2+20201114-4 patch=2.7.6-7 perl=5.32.1-5 perl-base=5.32.1-5 perl-modules-5.32=5.32.1-5 po-debconf=1.0.21+nmu1 rpcsvc-proto=1.4.2-4 sed=4.7-1 sensible-utils=0.0.16 sysvinit-utils=2.96-7 tabix=1.13+ds-1 tar=1.34+dfsg-1 util-linux=2.37.2-1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210902T030735Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210902T030735Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210827T161311Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d bcftools=1.13-1 && mkdir -p /build/bcftools-L9x9Cm && dpkg-source --no-check -x /*.dsc /build/bcftools-L9x9Cm/bcftools-1.13 && chown -R builduser:builduser /build/bcftools-L9x9Cm" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bcftools-L9x9Cm/bcftools-1.13 && env DEB_BUILD_OPTIONS="parallel=12" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1630075014" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/bcftools-L9x9Cm /tmp/bcftools-1.13-154vetjdw bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20210827T161311Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.LzPNBxJKvK as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.LzPNBxJKvK Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210827T161311Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210827T161311Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (774 kB/s) Selecting previously unselected package libfakeroot: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 ... 4670 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-17) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210902T030735Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210902T030735Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210827T161311Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.LzPNBxJKvK Get:1 http://snapshot.notset.fr/archive/debian/20210902T030735Z bookworm InRelease [112 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210827T161311Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210902T030735Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210902T030735Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210902T030735Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210902T030735Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210902T030735Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210902T030735Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210902T030735Z bookworm/main Sources [11.6 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210902T030735Z bookworm/main amd64 Packages [11.3 MB] Fetched 23.0 MB in 21s (1079 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.LzPNBxJKvK I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d bcftools=1.13-1 && mkdir -p /build/bcftools-L9x9Cm && dpkg-source --no-check -x /*.dsc /build/bcftools-L9x9Cm/bcftools-1.13 && chown -R builduser:builduser /build/bcftools-L9x9Cm"' exec /tmp/mmdebstrap.LzPNBxJKvK Reading package lists... NOTICE: 'bcftools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bcftools.git Please use: git clone https://salsa.debian.org/med-team/bcftools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3143 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210902T030735Z bookworm/main bcftools 1.13-1 (dsc) [2154 B] Get:2 http://snapshot.notset.fr/archive/debian/20210902T030735Z bookworm/main bcftools 1.13-1 (tar) [3134 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210902T030735Z bookworm/main bcftools 1.13-1 (diff) [7212 B] Fetched 3143 kB in 3s (1240 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'bcftools_1.13-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting bcftools in /build/bcftools-L9x9Cm/bcftools-1.13 dpkg-source: info: unpacking bcftools_1.13.orig.tar.gz dpkg-source: info: unpacking bcftools_1.13-1.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 dpkg-source: info: applying 2to3.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bcftools-L9x9Cm/bcftools-1.13 && env DEB_BUILD_OPTIONS="parallel=12" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1630075014" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.LzPNBxJKvK dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.13-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean rm -f config.mk && touch config.mk dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/bcftools-L9x9Cm/bcftools-1.13' dh_auto_clean make -j12 distclean make[2]: Entering directory '/build/bcftools-L9x9Cm/bcftools-1.13' rm -f test/*.o test/*.fa.fai test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -f test/*.unsorted.hex test/*.unsorted.tsv rm -rf plugins/*.dSYM rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/build/bcftools-L9x9Cm/bcftools-1.13' rm -f test/mpileup/indel-AD.1.out.new test/view-t.1.out.new test/view-t.2.out.new make[1]: Leaving directory '/build/bcftools-L9x9Cm/bcftools-1.13' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/build/bcftools-L9x9Cm/bcftools-1.13' 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.m4:1096: 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-L9x9Cm/bcftools-1.13' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bcftools-L9x9Cm/bcftools-1.13' 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-option-checking --disable-silent-rules --libdir=\${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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/bcftools-L9x9Cm/bcftools-1.13' dh_auto_build -a make -j12 make[1]: Entering directory '/build/bcftools-L9x9Cm/bcftools-1.13' echo '#define BCFTOOLS_VERSION "1.13"' > version.h gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 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-ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/add-variantkey.so version.c plugins/add-variantkey.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/allele-length.so version.c plugins/allele-length.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/gvcfz.so version.c plugins/gvcfz.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/indel-stats.so version.c plugins/indel-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/parental-origin.so version.c plugins/parental-origin.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/scatter.so version.c plugins/scatter.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split-vep.so version.c plugins/split-vep.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c -ldl gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -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-L9x9Cm/bcftools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c -ldl gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-L9x9Cm/bcftools-1.13=. -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 gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -ldl gcc -rdynamic -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 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 cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o vcfplugin.o -lhts -lm -lz -ldl -lpthread make[1]: Leaving directory '/build/bcftools-L9x9Cm/bcftools-1.13' debian/rules override_dh_auto_test make[1]: Entering directory '/build/bcftools-L9x9Cm/bcftools-1.13' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/bcftools-L9x9Cm/bcftools-1.13' ./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 --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} 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/TNe9AYj4ek/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H /tmp/TNe9AYj4ek/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/TNe9AYj4ek/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H /tmp/TNe9AYj4ek/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H /tmp/TNe9AYj4ek/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H /tmp/TNe9AYj4ek/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H /tmp/TNe9AYj4ek/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H /tmp/TNe9AYj4ek/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H /tmp/TNe9AYj4ek/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H /tmp/TNe9AYj4ek/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H /tmp/TNe9AYj4ek/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H /tmp/TNe9AYj4ek/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H /tmp/TNe9AYj4ek/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H /tmp/TNe9AYj4ek/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -s /tmp/TNe9AYj4ek/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -s /tmp/TNe9AYj4ek/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -s /tmp/TNe9AYj4ek/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -n /tmp/TNe9AYj4ek/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -n /tmp/TNe9AYj4ek/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -n /tmp/TNe9AYj4ek/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -n /tmp/TNe9AYj4ek/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -n /tmp/TNe9AYj4ek/idx.bcf.csi .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -s /tmp/TNe9AYj4ek/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -s /tmp/TNe9AYj4ek/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -s /tmp/TNe9AYj4ek/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -n /tmp/TNe9AYj4ek/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -n /tmp/TNe9AYj4ek/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -n /tmp/TNe9AYj4ek/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -n /tmp/TNe9AYj4ek/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools index -n /tmp/TNe9AYj4ek/empty.bcf.csi .. ok test_vcf_check: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools stats -s - /tmp/TNe9AYj4ek/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/check.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/bcftools-L9x9Cm/bcftools-1.13/misc/plot-vcfstats -m /tmp/TNe9AYj4ek/check.1.chk /tmp/TNe9AYj4ek/check.2.chk /tmp/TNe9AYj4ek/check.3.chk /tmp/TNe9AYj4ek/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools stats -s - /tmp/TNe9AYj4ek/stats.a.vcf.gz /tmp/TNe9AYj4ek/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools stats -s B /tmp/TNe9AYj4ek/stats.a.vcf.gz /tmp/TNe9AYj4ek/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools stats -s - /tmp/TNe9AYj4ek/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -n =2 /tmp/TNe9AYj4ek/isec.a.vcf.gz /tmp/TNe9AYj4ek/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -Ob -n =2 /tmp/TNe9AYj4ek/isec.a.vcf.gz /tmp/TNe9AYj4ek/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/TNe9AYj4ek/isec.a.vcf.gz /tmp/TNe9AYj4ek/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/TNe9AYj4ek/isec.a.vcf.gz /tmp/TNe9AYj4ek/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -n =2 -c both /tmp/TNe9AYj4ek/isec.a.vcf.gz /tmp/TNe9AYj4ek/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -Ob -n =2 -c both /tmp/TNe9AYj4ek/isec.a.vcf.gz /tmp/TNe9AYj4ek/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -n =2 -c any /tmp/TNe9AYj4ek/isec.a.vcf.gz /tmp/TNe9AYj4ek/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -Ob -n =2 -c any /tmp/TNe9AYj4ek/isec.a.vcf.gz /tmp/TNe9AYj4ek/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -C -c any /tmp/TNe9AYj4ek/isec.a.vcf.gz /tmp/TNe9AYj4ek/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -Ob -C -c any /tmp/TNe9AYj4ek/isec.a.vcf.gz /tmp/TNe9AYj4ek/isec.b.vcf.gz .. ok test_vcf_isec2: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec --no-version -T /tmp/TNe9AYj4ek/isec.tab.gz /tmp/TNe9AYj4ek/isec.a.vcf.gz .. ok test_vcf_isec2: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -Ob -T /tmp/TNe9AYj4ek/isec.tab.gz /tmp/TNe9AYj4ek/isec.a.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/TNe9AYj4ek/isec-miss.1.1.vcf.gz /tmp/TNe9AYj4ek/isec-miss.1.2.vcf.gz /tmp/TNe9AYj4ek/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/TNe9AYj4ek/isec-miss.1.1.vcf.gz /tmp/TNe9AYj4ek/isec-miss.1.2.vcf.gz /tmp/TNe9AYj4ek/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -R /build/bcftools-L9x9Cm/bcftools-1.13/test/isec-miss.1.regs.txt -n +1 /tmp/TNe9AYj4ek/isec-miss.1.1.vcf.gz /tmp/TNe9AYj4ek/isec-miss.1.2.vcf.gz /tmp/TNe9AYj4ek/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -Ob -R /build/bcftools-L9x9Cm/bcftools-1.13/test/isec-miss.1.regs.txt -n +1 /tmp/TNe9AYj4ek/isec-miss.1.1.vcf.gz /tmp/TNe9AYj4ek/isec-miss.1.2.vcf.gz /tmp/TNe9AYj4ek/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/TNe9AYj4ek/isec-miss.2.1.vcf.gz /tmp/TNe9AYj4ek/isec-miss.2.2.vcf.gz /tmp/TNe9AYj4ek/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/TNe9AYj4ek/isec-miss.2.1.vcf.gz /tmp/TNe9AYj4ek/isec-miss.2.2.vcf.gz /tmp/TNe9AYj4ek/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -R /build/bcftools-L9x9Cm/bcftools-1.13/test/isec-miss.1.regs.txt -n +1 /tmp/TNe9AYj4ek/isec-miss.2.1.vcf.gz /tmp/TNe9AYj4ek/isec-miss.2.2.vcf.gz /tmp/TNe9AYj4ek/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools isec -Ob -R /build/bcftools-L9x9Cm/bcftools-1.13/test/isec-miss.1.regs.txt -n +1 /tmp/TNe9AYj4ek/isec-miss.2.1.vcf.gz /tmp/TNe9AYj4ek/isec-miss.2.2.vcf.gz /tmp/TNe9AYj4ek/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version -i AF:join /tmp/TNe9AYj4ek/merge.join.a.vcf.gz /tmp/TNe9AYj4ek/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob -i AF:join /tmp/TNe9AYj4ek/merge.join.a.vcf.gz /tmp/TNe9AYj4ek/merge.join.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version -i AF:join /tmp/TNe9AYj4ek/merge.join.a.bcf /tmp/TNe9AYj4ek/merge.join.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob -i AF:join /tmp/TNe9AYj4ek/merge.join.a.bcf /tmp/TNe9AYj4ek/merge.join.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/TNe9AYj4ek/merge.LPL.a.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.b.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/TNe9AYj4ek/merge.LPL.a.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.b.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.c.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/TNe9AYj4ek/merge.LPL.a.bcf /tmp/TNe9AYj4ek/merge.LPL.b.bcf /tmp/TNe9AYj4ek/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/TNe9AYj4ek/merge.LPL.a.bcf /tmp/TNe9AYj4ek/merge.LPL.b.bcf /tmp/TNe9AYj4ek/merge.LPL.c.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -L 1 /tmp/TNe9AYj4ek/merge.LPL.a.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.b.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -L 1 /tmp/TNe9AYj4ek/merge.LPL.a.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.b.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.c.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -L 1 /tmp/TNe9AYj4ek/merge.LPL.a.bcf /tmp/TNe9AYj4ek/merge.LPL.b.bcf /tmp/TNe9AYj4ek/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -L 1 /tmp/TNe9AYj4ek/merge.LPL.a.bcf /tmp/TNe9AYj4ek/merge.LPL.b.bcf /tmp/TNe9AYj4ek/merge.LPL.c.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -L 2 /tmp/TNe9AYj4ek/merge.LPL.a.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.b.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -L 2 /tmp/TNe9AYj4ek/merge.LPL.a.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.b.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.c.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -L 2 /tmp/TNe9AYj4ek/merge.LPL.a.bcf /tmp/TNe9AYj4ek/merge.LPL.b.bcf /tmp/TNe9AYj4ek/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -L 2 /tmp/TNe9AYj4ek/merge.LPL.a.bcf /tmp/TNe9AYj4ek/merge.LPL.b.bcf /tmp/TNe9AYj4ek/merge.LPL.c.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -L 3 /tmp/TNe9AYj4ek/merge.LPL.a.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.b.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -L 3 /tmp/TNe9AYj4ek/merge.LPL.a.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.b.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.c.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -L 3 /tmp/TNe9AYj4ek/merge.LPL.a.bcf /tmp/TNe9AYj4ek/merge.LPL.b.bcf /tmp/TNe9AYj4ek/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -L 3 /tmp/TNe9AYj4ek/merge.LPL.a.bcf /tmp/TNe9AYj4ek/merge.LPL.b.bcf /tmp/TNe9AYj4ek/merge.LPL.c.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -L 4 /tmp/TNe9AYj4ek/merge.LPL.a.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.b.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -L 4 /tmp/TNe9AYj4ek/merge.LPL.a.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.b.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.c.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -L 4 /tmp/TNe9AYj4ek/merge.LPL.a.bcf /tmp/TNe9AYj4ek/merge.LPL.b.bcf /tmp/TNe9AYj4ek/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -L 4 /tmp/TNe9AYj4ek/merge.LPL.a.bcf /tmp/TNe9AYj4ek/merge.LPL.b.bcf /tmp/TNe9AYj4ek/merge.LPL.c.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -L 5 /tmp/TNe9AYj4ek/merge.LPL.a.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.b.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -L 5 /tmp/TNe9AYj4ek/merge.LPL.a.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.b.vcf.gz /tmp/TNe9AYj4ek/merge.LPL.c.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -L 5 /tmp/TNe9AYj4ek/merge.LPL.a.bcf /tmp/TNe9AYj4ek/merge.LPL.b.bcf /tmp/TNe9AYj4ek/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -L 5 /tmp/TNe9AYj4ek/merge.LPL.a.bcf /tmp/TNe9AYj4ek/merge.LPL.b.bcf /tmp/TNe9AYj4ek/merge.LPL.c.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/TNe9AYj4ek/merge.a.vcf.gz /tmp/TNe9AYj4ek/merge.b.vcf.gz /tmp/TNe9AYj4ek/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/TNe9AYj4ek/merge.a.vcf.gz /tmp/TNe9AYj4ek/merge.b.vcf.gz /tmp/TNe9AYj4ek/merge.c.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/TNe9AYj4ek/merge.a.bcf /tmp/TNe9AYj4ek/merge.b.bcf /tmp/TNe9AYj4ek/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/TNe9AYj4ek/merge.a.bcf /tmp/TNe9AYj4ek/merge.b.bcf /tmp/TNe9AYj4ek/merge.c.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -Fx /tmp/TNe9AYj4ek/merge.a.vcf.gz /tmp/TNe9AYj4ek/merge.b.vcf.gz /tmp/TNe9AYj4ek/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -Fx /tmp/TNe9AYj4ek/merge.a.vcf.gz /tmp/TNe9AYj4ek/merge.b.vcf.gz /tmp/TNe9AYj4ek/merge.c.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -Fx /tmp/TNe9AYj4ek/merge.a.bcf /tmp/TNe9AYj4ek/merge.b.bcf /tmp/TNe9AYj4ek/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -Fx /tmp/TNe9AYj4ek/merge.a.bcf /tmp/TNe9AYj4ek/merge.b.bcf /tmp/TNe9AYj4ek/merge.c.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -0 /tmp/TNe9AYj4ek/merge.a.vcf.gz /tmp/TNe9AYj4ek/merge.b.vcf.gz /tmp/TNe9AYj4ek/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -0 /tmp/TNe9AYj4ek/merge.a.vcf.gz /tmp/TNe9AYj4ek/merge.b.vcf.gz /tmp/TNe9AYj4ek/merge.c.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -0 /tmp/TNe9AYj4ek/merge.a.bcf /tmp/TNe9AYj4ek/merge.b.bcf /tmp/TNe9AYj4ek/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -0 /tmp/TNe9AYj4ek/merge.a.bcf /tmp/TNe9AYj4ek/merge.b.bcf /tmp/TNe9AYj4ek/merge.c.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -m none /tmp/TNe9AYj4ek/merge.2.a.vcf.gz /tmp/TNe9AYj4ek/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -m none /tmp/TNe9AYj4ek/merge.2.a.vcf.gz /tmp/TNe9AYj4ek/merge.2.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -m none /tmp/TNe9AYj4ek/merge.2.a.bcf /tmp/TNe9AYj4ek/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -m none /tmp/TNe9AYj4ek/merge.2.a.bcf /tmp/TNe9AYj4ek/merge.2.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -m both /tmp/TNe9AYj4ek/merge.2.a.vcf.gz /tmp/TNe9AYj4ek/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -m both /tmp/TNe9AYj4ek/merge.2.a.vcf.gz /tmp/TNe9AYj4ek/merge.2.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -m both /tmp/TNe9AYj4ek/merge.2.a.bcf /tmp/TNe9AYj4ek/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -m both /tmp/TNe9AYj4ek/merge.2.a.bcf /tmp/TNe9AYj4ek/merge.2.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -m all /tmp/TNe9AYj4ek/merge.2.a.vcf.gz /tmp/TNe9AYj4ek/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -m all /tmp/TNe9AYj4ek/merge.2.a.vcf.gz /tmp/TNe9AYj4ek/merge.2.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -m all /tmp/TNe9AYj4ek/merge.2.a.bcf /tmp/TNe9AYj4ek/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -m all /tmp/TNe9AYj4ek/merge.2.a.bcf /tmp/TNe9AYj4ek/merge.2.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/TNe9AYj4ek/merge.3.a.vcf.gz /tmp/TNe9AYj4ek/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/TNe9AYj4ek/merge.3.a.vcf.gz /tmp/TNe9AYj4ek/merge.3.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/TNe9AYj4ek/merge.3.a.bcf /tmp/TNe9AYj4ek/merge.3.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/TNe9AYj4ek/merge.3.a.bcf /tmp/TNe9AYj4ek/merge.3.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -m id /tmp/TNe9AYj4ek/merge.4.a.vcf.gz /tmp/TNe9AYj4ek/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -m id /tmp/TNe9AYj4ek/merge.4.a.vcf.gz /tmp/TNe9AYj4ek/merge.4.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples -m id /tmp/TNe9AYj4ek/merge.4.a.bcf /tmp/TNe9AYj4ek/merge.4.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples -m id /tmp/TNe9AYj4ek/merge.4.a.bcf /tmp/TNe9AYj4ek/merge.4.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/TNe9AYj4ek/gvcf.merge.1.vcf.gz /tmp/TNe9AYj4ek/gvcf.merge.2.vcf.gz /tmp/TNe9AYj4ek/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/TNe9AYj4ek/gvcf.merge.1.vcf.gz /tmp/TNe9AYj4ek/gvcf.merge.2.vcf.gz /tmp/TNe9AYj4ek/gvcf.merge.3.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/TNe9AYj4ek/gvcf.merge.1.bcf /tmp/TNe9AYj4ek/gvcf.merge.2.bcf /tmp/TNe9AYj4ek/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/TNe9AYj4ek/gvcf.merge.1.bcf /tmp/TNe9AYj4ek/gvcf.merge.2.bcf /tmp/TNe9AYj4ek/gvcf.merge.3.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.2.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.2.b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.2.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.2.b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.2.c.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf - -i SRC:join /tmp/TNe9AYj4ek/merge.gvcf.3.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf - -i SRC:join /tmp/TNe9AYj4ek/merge.gvcf.3.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.3.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.4.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.4.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.4.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.4.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.4.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.4.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version /tmp/TNe9AYj4ek/merge.5.a.vcf.gz /tmp/TNe9AYj4ek/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob /tmp/TNe9AYj4ek/merge.5.a.vcf.gz /tmp/TNe9AYj4ek/merge.5.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version /tmp/TNe9AYj4ek/merge.5.a.bcf /tmp/TNe9AYj4ek/merge.5.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob /tmp/TNe9AYj4ek/merge.5.a.bcf /tmp/TNe9AYj4ek/merge.5.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version /tmp/TNe9AYj4ek/merge.6.a.vcf.gz /tmp/TNe9AYj4ek/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob /tmp/TNe9AYj4ek/merge.6.a.vcf.gz /tmp/TNe9AYj4ek/merge.6.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version /tmp/TNe9AYj4ek/merge.6.a.bcf /tmp/TNe9AYj4ek/merge.6.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob /tmp/TNe9AYj4ek/merge.6.a.bcf /tmp/TNe9AYj4ek/merge.6.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.7.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.7.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.7.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.7.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.7.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.7.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.8.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.8.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.8.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.8.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/TNe9AYj4ek/merge.gvcf.8.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.8.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/TNe9AYj4ek/merge.7.a.vcf.gz /tmp/TNe9AYj4ek/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/TNe9AYj4ek/merge.7.a.vcf.gz /tmp/TNe9AYj4ek/merge.7.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/TNe9AYj4ek/merge.7.a.bcf /tmp/TNe9AYj4ek/merge.7.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/TNe9AYj4ek/merge.7.a.bcf /tmp/TNe9AYj4ek/merge.7.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa /tmp/TNe9AYj4ek/merge.gvcf.9a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9c.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa /tmp/TNe9AYj4ek/merge.gvcf.9a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9c.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9d.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa /tmp/TNe9AYj4ek/merge.gvcf.9a.bcf /tmp/TNe9AYj4ek/merge.gvcf.9b.bcf /tmp/TNe9AYj4ek/merge.gvcf.9c.bcf /tmp/TNe9AYj4ek/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa /tmp/TNe9AYj4ek/merge.gvcf.9a.bcf /tmp/TNe9AYj4ek/merge.gvcf.9b.bcf /tmp/TNe9AYj4ek/merge.gvcf.9c.bcf /tmp/TNe9AYj4ek/merge.gvcf.9d.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/TNe9AYj4ek/merge.gvcf.9a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9c.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/TNe9AYj4ek/merge.gvcf.9a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9c.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9d.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/TNe9AYj4ek/merge.gvcf.9a.bcf /tmp/TNe9AYj4ek/merge.gvcf.9b.bcf /tmp/TNe9AYj4ek/merge.gvcf.9c.bcf /tmp/TNe9AYj4ek/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/TNe9AYj4ek/merge.gvcf.9a.bcf /tmp/TNe9AYj4ek/merge.gvcf.9b.bcf /tmp/TNe9AYj4ek/merge.gvcf.9c.bcf /tmp/TNe9AYj4ek/merge.gvcf.9d.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa /tmp/TNe9AYj4ek/merge.gvcf.9a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9c.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9d.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa /tmp/TNe9AYj4ek/merge.gvcf.9a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9c.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9d.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9e.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa /tmp/TNe9AYj4ek/merge.gvcf.9a.bcf /tmp/TNe9AYj4ek/merge.gvcf.9b.bcf /tmp/TNe9AYj4ek/merge.gvcf.9c.bcf /tmp/TNe9AYj4ek/merge.gvcf.9d.bcf /tmp/TNe9AYj4ek/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa /tmp/TNe9AYj4ek/merge.gvcf.9a.bcf /tmp/TNe9AYj4ek/merge.gvcf.9b.bcf /tmp/TNe9AYj4ek/merge.gvcf.9c.bcf /tmp/TNe9AYj4ek/merge.gvcf.9d.bcf /tmp/TNe9AYj4ek/merge.gvcf.9e.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/TNe9AYj4ek/merge.gvcf.9a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9c.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9d.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/TNe9AYj4ek/merge.gvcf.9a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9c.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9d.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.9e.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/TNe9AYj4ek/merge.gvcf.9a.bcf /tmp/TNe9AYj4ek/merge.gvcf.9b.bcf /tmp/TNe9AYj4ek/merge.gvcf.9c.bcf /tmp/TNe9AYj4ek/merge.gvcf.9d.bcf /tmp/TNe9AYj4ek/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --gvcf /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/TNe9AYj4ek/merge.gvcf.9a.bcf /tmp/TNe9AYj4ek/merge.gvcf.9b.bcf /tmp/TNe9AYj4ek/merge.gvcf.9c.bcf /tmp/TNe9AYj4ek/merge.gvcf.9d.bcf /tmp/TNe9AYj4ek/merge.gvcf.9e.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version /tmp/TNe9AYj4ek/merge.gvcf.10.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob /tmp/TNe9AYj4ek/merge.gvcf.10.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.10.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version /tmp/TNe9AYj4ek/merge.gvcf.10.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob /tmp/TNe9AYj4ek/merge.gvcf.10.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.10.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version -m none /tmp/TNe9AYj4ek/merge.gvcf.10.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob -m none /tmp/TNe9AYj4ek/merge.gvcf.10.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.10.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version -m none /tmp/TNe9AYj4ek/merge.gvcf.10.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob -m none /tmp/TNe9AYj4ek/merge.gvcf.10.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.10.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa /tmp/TNe9AYj4ek/merge.gvcf.10.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa /tmp/TNe9AYj4ek/merge.gvcf.10.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.10.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa /tmp/TNe9AYj4ek/merge.gvcf.10.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa /tmp/TNe9AYj4ek/merge.gvcf.10.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.10.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/TNe9AYj4ek/merge.gvcf.10.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/TNe9AYj4ek/merge.gvcf.10.a.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.10.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/TNe9AYj4ek/merge.gvcf.10.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/TNe9AYj4ek/merge.gvcf.10.a.bcf /tmp/TNe9AYj4ek/merge.gvcf.10.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa /tmp/TNe9AYj4ek/merge.gvcf.10.b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa /tmp/TNe9AYj4ek/merge.gvcf.10.b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.10.a.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa /tmp/TNe9AYj4ek/merge.gvcf.10.b.bcf /tmp/TNe9AYj4ek/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa /tmp/TNe9AYj4ek/merge.gvcf.10.b.bcf /tmp/TNe9AYj4ek/merge.gvcf.10.a.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/TNe9AYj4ek/merge.gvcf.10.b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/TNe9AYj4ek/merge.gvcf.10.b.vcf.gz /tmp/TNe9AYj4ek/merge.gvcf.10.a.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/TNe9AYj4ek/merge.gvcf.10.b.bcf /tmp/TNe9AYj4ek/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob -g /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/TNe9AYj4ek/merge.gvcf.10.b.bcf /tmp/TNe9AYj4ek/merge.gvcf.10.a.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version /tmp/TNe9AYj4ek/merge.noidx.a.vcf.gz /tmp/TNe9AYj4ek/merge.noidx.b.vcf.gz /tmp/TNe9AYj4ek/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob /tmp/TNe9AYj4ek/merge.noidx.a.vcf.gz /tmp/TNe9AYj4ek/merge.noidx.b.vcf.gz /tmp/TNe9AYj4ek/merge.noidx.c.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version /tmp/TNe9AYj4ek/merge.noidx.a.bcf /tmp/TNe9AYj4ek/merge.noidx.b.bcf /tmp/TNe9AYj4ek/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob /tmp/TNe9AYj4ek/merge.noidx.a.bcf /tmp/TNe9AYj4ek/merge.noidx.b.bcf /tmp/TNe9AYj4ek/merge.noidx.c.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --no-index /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.noidx.a.vcf /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.noidx.b.vcf /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --no-index /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.noidx.a.vcf /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.noidx.b.vcf /build/bcftools-L9x9Cm/bcftools-1.13/test/merge.noidx.c.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge --no-version --no-index /tmp/TNe9AYj4ek/merge.noidx.a.bcf /tmp/TNe9AYj4ek/merge.noidx.b.bcf /tmp/TNe9AYj4ek/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools merge -Ob --no-index /tmp/TNe9AYj4ek/merge.noidx.a.bcf /tmp/TNe9AYj4ek/merge.noidx.b.bcf /tmp/TNe9AYj4ek/merge.noidx.c.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/TNe9AYj4ek/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.string.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/TNe9AYj4ek/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.string.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/TNe9AYj4ek/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.string.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/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-L9x9Cm/bcftools-1.13/bcftools query -f '%RSX\t%VKX\n' /tmp/TNe9AYj4ek/query.variantkey.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.variantkey.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/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/TNe9AYj4ek/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.vectors.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/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-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/TNe9AYj4ek/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/TNe9AYj4ek/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/TNe9AYj4ek/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/TNe9AYj4ek/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/TNe9AYj4ek/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/TNe9AYj4ek/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/filter.11.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/TNe9AYj4ek/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/filter.11.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/TNe9AYj4ek/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/filter.11.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/TNe9AYj4ek/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/filter.11.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%LINE' /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%LINE' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/TNe9AYj4ek/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter-type.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/TNe9AYj4ek/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter-type.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/TNe9AYj4ek/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter-type.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/TNe9AYj4ek/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter-type.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/TNe9AYj4ek/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter-type.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/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/TNe9AYj4ek/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/filter-missing-floats.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/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-L9x9Cm/bcftools-1.13/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/TNe9AYj4ek/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/filter-missing-floats.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/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-L9x9Cm/bcftools-1.13/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/TNe9AYj4ek/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/TNe9AYj4ek/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/TNe9AYj4ek/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/filter.5.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/TNe9AYj4ek/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/filter.5.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.filter.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/TNe9AYj4ek/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.3.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/TNe9AYj4ek/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.3.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/TNe9AYj4ek/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.3.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/TNe9AYj4ek/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/filter.5.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/TNe9AYj4ek/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.4.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-L9x9Cm/bcftools-1.13/test/query.56.out' /tmp/TNe9AYj4ek/view.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-L9x9Cm/bcftools-1.13/test/query.56.out' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/TNe9AYj4ek/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.5.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/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-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/TNe9AYj4ek/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.5.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/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-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/TNe9AYj4ek/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.5.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/TNe9AYj4ek/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.negative.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/TNe9AYj4ek/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.negative.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/TNe9AYj4ek/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.negative.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/TNe9AYj4ek/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.negative.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/TNe9AYj4ek/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.11.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/TNe9AYj4ek/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.11.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/TNe9AYj4ek/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.11.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/TNe9AYj4ek/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.11.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/TNe9AYj4ek/query.filter.6.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.6.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/TNe9AYj4ek/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.7.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/TNe9AYj4ek/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.7.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/TNe9AYj4ek/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.7.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/TNe9AYj4ek/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.7.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/TNe9AYj4ek/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.7.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/TNe9AYj4ek/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.7.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/TNe9AYj4ek/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.7.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/TNe9AYj4ek/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.7.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/TNe9AYj4ek/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.8.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/TNe9AYj4ek/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.8.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/TNe9AYj4ek/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.9.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/TNe9AYj4ek/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.9.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/TNe9AYj4ek/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.10.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/TNe9AYj4ek/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.10.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/TNe9AYj4ek/query.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/TNe9AYj4ek/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.12.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/TNe9AYj4ek/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/query.filter.12.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -cx -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.fa /tmp/TNe9AYj4ek/norm.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -cx -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.fa /tmp/TNe9AYj4ek/norm.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -m- /tmp/TNe9AYj4ek/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -m- /tmp/TNe9AYj4ek/norm.split.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -m- /tmp/TNe9AYj4ek/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -m- /tmp/TNe9AYj4ek/norm.split.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -m- --force /tmp/TNe9AYj4ek/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -m- --force /tmp/TNe9AYj4ek/norm.split.3.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -m- /tmp/TNe9AYj4ek/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -m- /tmp/TNe9AYj4ek/norm.split.4.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -m- --keep-sum AD /tmp/TNe9AYj4ek/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -m- --keep-sum AD /tmp/TNe9AYj4ek/norm.split.4.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -m- -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.fa /tmp/TNe9AYj4ek/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -m- -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.fa /tmp/TNe9AYj4ek/norm.split.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -m+ /tmp/TNe9AYj4ek/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -m+ /tmp/TNe9AYj4ek/norm.merge.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -m+ /tmp/TNe9AYj4ek/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -m+ /tmp/TNe9AYj4ek/norm.merge.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -m+ /tmp/TNe9AYj4ek/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -m+ /tmp/TNe9AYj4ek/norm.merge.3.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -m+ -s /tmp/TNe9AYj4ek/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -m+ -s /tmp/TNe9AYj4ek/norm.merge.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -Nc s -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.fa /tmp/TNe9AYj4ek/norm.setref.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -Nc s -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.fa /tmp/TNe9AYj4ek/norm.setref.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.fa /tmp/TNe9AYj4ek/norm.telomere.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.fa /tmp/TNe9AYj4ek/norm.telomere.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -d snps /tmp/TNe9AYj4ek/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -d snps /tmp/TNe9AYj4ek/norm.rmdup.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -d indels /tmp/TNe9AYj4ek/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -d indels /tmp/TNe9AYj4ek/norm.rmdup.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -d both /tmp/TNe9AYj4ek/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -d both /tmp/TNe9AYj4ek/norm.rmdup.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -d all /tmp/TNe9AYj4ek/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -d all /tmp/TNe9AYj4ek/norm.rmdup.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -d none /tmp/TNe9AYj4ek/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -d none /tmp/TNe9AYj4ek/norm.rmdup.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -d exact /tmp/TNe9AYj4ek/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -d exact /tmp/TNe9AYj4ek/norm.rmdup.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -d none /tmp/TNe9AYj4ek/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -d none /tmp/TNe9AYj4ek/norm.rmdup.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -d exact /tmp/TNe9AYj4ek/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -d exact /tmp/TNe9AYj4ek/norm.rmdup.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -d indels /tmp/TNe9AYj4ek/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -d indels /tmp/TNe9AYj4ek/norm.rmdup.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -d any /tmp/TNe9AYj4ek/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -d any /tmp/TNe9AYj4ek/norm.rmdup.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -d both /tmp/TNe9AYj4ek/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -d both /tmp/TNe9AYj4ek/norm.rmdup.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -d snps /tmp/TNe9AYj4ek/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -d snps /tmp/TNe9AYj4ek/norm.rmdup.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.2.fa /tmp/TNe9AYj4ek/norm.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.2.fa /tmp/TNe9AYj4ek/norm.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -c s -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.iupac.fa /tmp/TNe9AYj4ek/norm.iupac.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -c s -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.iupac.fa /tmp/TNe9AYj4ek/norm.iupac.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version -c s -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.3.fa /tmp/TNe9AYj4ek/norm.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob -c s -f /build/bcftools-L9x9Cm/bcftools-1.13/test/norm.3.fa /tmp/TNe9AYj4ek/norm.3.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/TNe9AYj4ek/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/TNe9AYj4ek/atomize.split.1.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/TNe9AYj4ek/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/TNe9AYj4ek/atomize.split.1.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/TNe9AYj4ek/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/TNe9AYj4ek/atomize.split.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/TNe9AYj4ek/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/TNe9AYj4ek/atomize.split.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/TNe9AYj4ek/view.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/TNe9AYj4ek/view.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -f PASS -Xks NA00003 /tmp/TNe9AYj4ek/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -f PASS -Xks NA00003 /tmp/TNe9AYj4ek/view.vcf.gz -r20,Y | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -xs NA00003 /tmp/TNe9AYj4ek/view.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -xs NA00003 /tmp/TNe9AYj4ek/view.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/TNe9AYj4ek/view.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/TNe9AYj4ek/view.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -p /tmp/TNe9AYj4ek/view.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -p /tmp/TNe9AYj4ek/view.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -P /tmp/TNe9AYj4ek/view.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -P /tmp/TNe9AYj4ek/view.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/TNe9AYj4ek/view.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/TNe9AYj4ek/view.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -Hu /tmp/TNe9AYj4ek/view.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -GVsnps /tmp/TNe9AYj4ek/view.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -GVsnps /tmp/TNe9AYj4ek/view.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/TNe9AYj4ek/view.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/TNe9AYj4ek/view.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -s ^NA00003 /tmp/TNe9AYj4ek/view.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -s ^NA00003 /tmp/TNe9AYj4ek/view.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version /tmp/TNe9AYj4ek/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/view.omitgenotypes.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -G /tmp/TNe9AYj4ek/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -G /tmp/TNe9AYj4ek/view.omitgenotypes.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -HG /tmp/TNe9AYj4ek/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -a /tmp/TNe9AYj4ek/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -a /tmp/TNe9AYj4ek/many.alleles.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -asA /tmp/TNe9AYj4ek/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -asA /tmp/TNe9AYj4ek/view.vectors.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -asB /tmp/TNe9AYj4ek/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -asB /tmp/TNe9AYj4ek/view.vectors.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -asA /tmp/TNe9AYj4ek/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -asA /tmp/TNe9AYj4ek/view.vectors.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -i'TXT0="text"' /tmp/TNe9AYj4ek/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -T /build/bcftools-L9x9Cm/bcftools-1.13/test/view.chrs.tab /tmp/TNe9AYj4ek/view.chrs.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -T /build/bcftools-L9x9Cm/bcftools-1.13/test/view.chrs.tab /tmp/TNe9AYj4ek/view.chrs.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -i 'POS>=3062917' /tmp/TNe9AYj4ek/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob -i 'POS>=3062917' /tmp/TNe9AYj4ek/filter.2.vcf.gz 1:3062917-3157410 | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/TNe9AYj4ek/idx.1.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/TNe9AYj4ek/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -R /build/bcftools-L9x9Cm/bcftools-1.13/test/idx.2.bed /tmp/TNe9AYj4ek/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -R /build/bcftools-L9x9Cm/bcftools-1.13/test/idx.3.bed /tmp/TNe9AYj4ek/idx.3.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -R /build/bcftools-L9x9Cm/bcftools-1.13/test/idx.4.bed /tmp/TNe9AYj4ek/idx.4.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -Ht 2 /tmp/TNe9AYj4ek/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -Ht 3 /tmp/TNe9AYj4ek/view-t.vcf.gz .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.1.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.1.vcf -Ou | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.2.vcf -Ou | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.4.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.4.vcf -Ou | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view /build/bcftools-L9x9Cm/bcftools-1.13/test/view64bit.5.vcf -Ou | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -C5:nonmajor /tmp/TNe9AYj4ek/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -c6:nonmajor /tmp/TNe9AYj4ek/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -q0.3:major /tmp/TNe9AYj4ek/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/TNe9AYj4ek/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/TNe9AYj4ek/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/TNe9AYj4ek/view.filter.annovar.vcf.gz .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mg0 /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mg0 /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.3.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.3.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.4.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.4.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.5.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.5.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv --ploidy-file /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ploidy -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv --ploidy-file /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ploidy -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.X.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv --ploidy-file /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ploidy -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ped /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv --ploidy-file /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ploidy -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ped /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.X.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv --ploidy-file /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ploidy -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.2.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv --ploidy-file /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ploidy -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.2.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.X.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.hwe.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.hwe.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.hwe.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.tab.gz /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.tab.gz /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.2.tab.gz /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.2.tab.gz /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.3.tab.gz -i /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.3.tab.gz -i /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.4.tab.gz -i /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.4.tab.gz -i /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.5.tab.gz -i /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.5.tab.gz -i /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.6.tab.gz -i /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.6.tab.gz -i /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.4.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.7.tab.gz -i /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.7.tab.gz -i /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.cals.1.tab.gz /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.cals.1.tab.gz /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.cals.1.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.cals.2.tab.gz /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/TNe9AYj4ek/mpileup.cals.2.tab.gz /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.cals.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -cv /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.c.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -cv /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.c.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -cv --ploidy-file /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ploidy -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -cv --ploidy-file /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ploidy -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.c.X.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -cv --ploidy-file /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ploidy -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ped /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -cv --ploidy-file /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ploidy -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ped /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.c.X.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -cv --ploidy-file /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ploidy -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.2.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -cv --ploidy-file /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.ploidy -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.2.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup.c.X.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv /build/bcftools-L9x9Cm/bcftools-1.13/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv /build/bcftools-L9x9Cm/bcftools-1.13/test/call-G.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-L9x9Cm/bcftools-1.13/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-L9x9Cm/bcftools-1.13/test/call-G.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -mv -F AN_POP,AC_POP /build/bcftools-L9x9Cm/bcftools-1.13/test/call-G.2.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -mv -F AN_POP,AC_POP /build/bcftools-L9x9Cm/bcftools-1.13/test/call-G.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -m /build/bcftools-L9x9Cm/bcftools-1.13/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -m /build/bcftools-L9x9Cm/bcftools-1.13/test/call.af-fixation.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -m -G /build/bcftools-L9x9Cm/bcftools-1.13/test/call.af-fixation.txt /build/bcftools-L9x9Cm/bcftools-1.13/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -m -G /build/bcftools-L9x9Cm/bcftools-1.13/test/call.af-fixation.txt /build/bcftools-L9x9Cm/bcftools-1.13/test/call.af-fixation.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call --no-version -m -G /build/bcftools-L9x9Cm/bcftools-1.13/test/call.af-fixation.txt -a GP,GQ /build/bcftools-L9x9Cm/bcftools-1.13/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools call -Ob -m -G /build/bcftools-L9x9Cm/bcftools-1.13/test/call.af-fixation.txt -a GP,GQ /build/bcftools-L9x9Cm/bcftools-1.13/test/call.af-fixation.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S. -e'TXT0="text"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S. -e'TXT0="text"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S. -e'FMT/STR="XX"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/bcftools-L9x9Cm/bcftools-1.13/test/view.filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -mx -g2 -G2 /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -mx -g2 -G2 /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.1.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -e'INFO/DP=19' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -e'INFO/DP=19' -s XX /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -e'INFO/DP=19' -s XX -mx /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' -s XX /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'ALT="."' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'ALT="."' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.4.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.4.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'GT="A"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'GT="A"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'GT="RR"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'GT="RR"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'GT="RA"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'GT="RA"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'GT="AR"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'GT="AR"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'GT="AA"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'GT="AA"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'GT="aA"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'GT="aA"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'GT="Aa"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'GT="Aa"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'GT="HOM"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'GT="HOM"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'GT="HET"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'GT="HET"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'GT="HAP"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'GT="HAP"' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'AD[:1]=11' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'AD[:1]=11' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'AD[1:]=11' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'AD[1:]=11' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'FR[0:1]=11' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'FR[0:1]=11' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'AD[*]="."' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'AD[*]="."' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'AD[0:0]=="."' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'AD[0:0]=="."' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'AD[0:0]!="."' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'AD[0:0]!="."' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'QUAL=="."' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'QUAL=="."' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'N_PASS(DP>32)=1' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'F_PASS(DP>32)=0.5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'F_MISSING>=1/5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.6.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'F_MISSING>=1/5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.6.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'F_MISSING>=0.2' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.6.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'F_MISSING>=0.2' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.6.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.6.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.6.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.6.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.6.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -mx -s + -g2:mnp,indel,other /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.7.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'FORMAT/AO==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i 'QUAL/FMT/AD==55' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.9.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i 'QUAL/INFO/AD==10' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.9.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.10.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.10.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.10.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-L9x9Cm/bcftools-1.13/test/filter.10.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools sort -m 0 /build/bcftools-L9x9Cm/bcftools-1.13/test/sort.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools sort -Ob -m 0 /build/bcftools-L9x9Cm/bcftools-1.13/test/sort.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools sort -m 1000 /build/bcftools-L9x9Cm/bcftools-1.13/test/sort.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools sort -Ob -m 1000 /build/bcftools-L9x9Cm/bcftools-1.13/test/sort.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-L9x9Cm/bcftools-1.13/test/regions.tab /tmp/TNe9AYj4ek/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/regions.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-L9x9Cm/bcftools-1.13/test/regions.tab .. ok test_vcf_regions: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/bcftools-L9x9Cm/bcftools-1.13/test/regions.tab /tmp/TNe9AYj4ek/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/TNe9AYj4ek/regions.tab.gz /tmp/TNe9AYj4ek/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/regions.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/TNe9AYj4ek/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/TNe9AYj4ek/regions.tab.gz /tmp/TNe9AYj4ek/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/TNe9AYj4ek/regions.bed /tmp/TNe9AYj4ek/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/regions.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/TNe9AYj4ek/regions.bed .. ok test_vcf_regions: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/TNe9AYj4ek/regions.bed /tmp/TNe9AYj4ek/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/TNe9AYj4ek/regions.bed.gz /tmp/TNe9AYj4ek/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/regions.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/TNe9AYj4ek/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/TNe9AYj4ek/regions.bed.gz /tmp/TNe9AYj4ek/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate2.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate2.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate2.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate2.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/TNe9AYj4ek/annotate.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/TNe9AYj4ek/annotate.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -x FORMAT /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -x FORMAT /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots4.vcf.gz -c +INFO /tmp/TNe9AYj4ek/annotate4.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots4.vcf.gz -c +INFO /tmp/TNe9AYj4ek/annotate4.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots4.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate4.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots4.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate4.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots10.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate10.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots10.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate10.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots11.vcf.gz -c FMT /tmp/TNe9AYj4ek/annotate11.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots11.vcf.gz -c FMT /tmp/TNe9AYj4ek/annotate11.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c FMT/newGT:=GT /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots2.vcf.gz -c FMT/newGT:=GT /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots12.vcf.gz -c FMT/GT:=newGT /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots12.vcf.gz -c FMT/GT:=newGT /tmp/TNe9AYj4ek/annotate2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots13.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate13.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots13.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate13.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots13.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate13.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots13.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate13.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots13.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate13.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots13.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate13.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -x FILTER/XX,INFO/XX --force /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate14.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate14.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate15.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate15.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate15.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate15.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate15.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate15.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate15.tab.gz -h /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate15.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -x FILTER /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate16.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -x FILTER /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate16.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate17.1.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate17.1.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate17.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate17.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate17.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate17.3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate18.1.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate18.1.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate18.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate18.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/TNe9AYj4ek/annotate19.dst.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/TNe9AYj4ek/annotate19.dst.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/TNe9AYj4ek/annotate19.dst.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/TNe9AYj4ek/annotate19.dst.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate20.src.vcf.gz -c FMT/GT /tmp/TNe9AYj4ek/annotate20.dst.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate20.src.vcf.gz -c FMT/GT /tmp/TNe9AYj4ek/annotate20.dst.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate20.src.vcf.gz -c +FMT/GT /tmp/TNe9AYj4ek/annotate20.dst.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate20.src.vcf.gz -c +FMT/GT /tmp/TNe9AYj4ek/annotate20.dst.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate20.src.vcf.gz -c -FMT/GT /tmp/TNe9AYj4ek/annotate20.dst.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate20.src.vcf.gz -c -FMT/GT /tmp/TNe9AYj4ek/annotate20.dst.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.multi.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.multi.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.missing-append.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.missing-append.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate9.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate9.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate --rename-annots /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate21.txt /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate21.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob --rename-annots /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate21.txt /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate21.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/TNe9AYj4ek/annotate22.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/TNe9AYj4ek/annotate22.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -a /tmp/TNe9AYj4ek/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate23.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate -Ob -a /tmp/TNe9AYj4ek/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate23.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat --no-version /tmp/TNe9AYj4ek/concat.1.a.vcf.gz /tmp/TNe9AYj4ek/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat -Ob /tmp/TNe9AYj4ek/concat.1.a.vcf.gz /tmp/TNe9AYj4ek/concat.1.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat --no-version /tmp/TNe9AYj4ek/concat.1.a.bcf /tmp/TNe9AYj4ek/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat -Ob /tmp/TNe9AYj4ek/concat.1.a.bcf /tmp/TNe9AYj4ek/concat.1.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat --no-version -a /tmp/TNe9AYj4ek/concat.2.a.vcf.gz /tmp/TNe9AYj4ek/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat -Ob -a /tmp/TNe9AYj4ek/concat.2.a.vcf.gz /tmp/TNe9AYj4ek/concat.2.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat --no-version -a /tmp/TNe9AYj4ek/concat.2.a.bcf /tmp/TNe9AYj4ek/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat -Ob -a /tmp/TNe9AYj4ek/concat.2.a.bcf /tmp/TNe9AYj4ek/concat.2.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat --no-version -aD /tmp/TNe9AYj4ek/concat.2.a.vcf.gz /tmp/TNe9AYj4ek/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat -Ob -aD /tmp/TNe9AYj4ek/concat.2.a.vcf.gz /tmp/TNe9AYj4ek/concat.2.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat --no-version -aD /tmp/TNe9AYj4ek/concat.2.a.bcf /tmp/TNe9AYj4ek/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat -Ob -aD /tmp/TNe9AYj4ek/concat.2.a.bcf /tmp/TNe9AYj4ek/concat.2.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat --no-version -l /tmp/TNe9AYj4ek/concat.3.a.vcf.gz /tmp/TNe9AYj4ek/concat.3.b.vcf.gz /tmp/TNe9AYj4ek/concat.3.0.vcf.gz /tmp/TNe9AYj4ek/concat.3.c.vcf.gz /tmp/TNe9AYj4ek/concat.3.d.vcf.gz /tmp/TNe9AYj4ek/concat.3.e.vcf.gz /tmp/TNe9AYj4ek/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat -Ob -l /tmp/TNe9AYj4ek/concat.3.a.vcf.gz /tmp/TNe9AYj4ek/concat.3.b.vcf.gz /tmp/TNe9AYj4ek/concat.3.0.vcf.gz /tmp/TNe9AYj4ek/concat.3.c.vcf.gz /tmp/TNe9AYj4ek/concat.3.d.vcf.gz /tmp/TNe9AYj4ek/concat.3.e.vcf.gz /tmp/TNe9AYj4ek/concat.3.f.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat --no-version -l /tmp/TNe9AYj4ek/concat.3.a.bcf /tmp/TNe9AYj4ek/concat.3.b.bcf /tmp/TNe9AYj4ek/concat.3.0.bcf /tmp/TNe9AYj4ek/concat.3.c.bcf /tmp/TNe9AYj4ek/concat.3.d.bcf /tmp/TNe9AYj4ek/concat.3.e.bcf /tmp/TNe9AYj4ek/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat -Ob -l /tmp/TNe9AYj4ek/concat.3.a.bcf /tmp/TNe9AYj4ek/concat.3.b.bcf /tmp/TNe9AYj4ek/concat.3.0.bcf /tmp/TNe9AYj4ek/concat.3.c.bcf /tmp/TNe9AYj4ek/concat.3.d.bcf /tmp/TNe9AYj4ek/concat.3.e.bcf /tmp/TNe9AYj4ek/concat.3.f.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1802741090 .. ok test_naive_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat --naive-force /tmp/TNe9AYj4ek/naive_concat.0.bcf /tmp/TNe9AYj4ek/naive_concat.1.bcf /tmp/TNe9AYj4ek/naive_concat.2.bcf /tmp/TNe9AYj4ek/naive_concat.3.bcf /tmp/TNe9AYj4ek/naive_concat.4.bcf /tmp/TNe9AYj4ek/naive_concat.5.bcf /tmp/TNe9AYj4ek/naive_concat.6.bcf /tmp/TNe9AYj4ek/naive_concat.7.bcf /tmp/TNe9AYj4ek/naive_concat.8.bcf /tmp/TNe9AYj4ek/naive_concat.9.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H .. ok test_naive_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat --naive /tmp/TNe9AYj4ek/naive_concat.0.vcf.gz /tmp/TNe9AYj4ek/naive_concat.1.vcf.gz /tmp/TNe9AYj4ek/naive_concat.2.vcf.gz /tmp/TNe9AYj4ek/naive_concat.3.vcf.gz /tmp/TNe9AYj4ek/naive_concat.4.vcf.gz /tmp/TNe9AYj4ek/naive_concat.5.vcf.gz /tmp/TNe9AYj4ek/naive_concat.6.vcf.gz /tmp/TNe9AYj4ek/naive_concat.7.vcf.gz /tmp/TNe9AYj4ek/naive_concat.8.vcf.gz /tmp/TNe9AYj4ek/naive_concat.9.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -H .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat --no-version -l /tmp/TNe9AYj4ek/concat.4.a.vcf.gz /tmp/TNe9AYj4ek/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat -Ob -l /tmp/TNe9AYj4ek/concat.4.a.vcf.gz /tmp/TNe9AYj4ek/concat.4.b.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat --no-version -l /tmp/TNe9AYj4ek/concat.4.a.bcf /tmp/TNe9AYj4ek/concat.4.b.bcf .. ok test_vcf_concat: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools concat -Ob -l /tmp/TNe9AYj4ek/concat.4.a.bcf /tmp/TNe9AYj4ek/concat.4.b.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.hdr /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.hdr | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.hdr /tmp/TNe9AYj4ek/reheader.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/TNe9AYj4ek/reheader.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.hdr | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.hdr /tmp/TNe9AYj4ek/reheader.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/TNe9AYj4ek/reheader.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.hdr | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples /tmp/TNe9AYj4ek/reheader.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/TNe9AYj4ek/reheader.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples /tmp/TNe9AYj4ek/reheader.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/TNe9AYj4ek/reheader.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples2 /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples2 | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples2 /tmp/TNe9AYj4ek/reheader.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/TNe9AYj4ek/reheader.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples2 | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples2 /tmp/TNe9AYj4ek/reheader.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/TNe9AYj4ek/reheader.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples2 | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples3 /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples3 | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples3 /tmp/TNe9AYj4ek/reheader.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/TNe9AYj4ek/reheader.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples3 | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples3 /tmp/TNe9AYj4ek/reheader.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/TNe9AYj4ek/reheader.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples3 | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples4 /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples4 | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples4 /tmp/TNe9AYj4ek/reheader.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/TNe9AYj4ek/reheader.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples4 | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples4 /tmp/TNe9AYj4ek/reheader.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/TNe9AYj4ek/reheader.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -s /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.samples4 | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.empty.hdr /build/bcftools-L9x9Cm/bcftools-1.13/test/empty.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-L9x9Cm/bcftools-1.13/test/empty.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.empty.hdr | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.empty.hdr /tmp/TNe9AYj4ek/empty.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/TNe9AYj4ek/empty.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.empty.hdr | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.empty.hdr /tmp/TNe9AYj4ek/empty.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/TNe9AYj4ek/empty.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.empty.hdr | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -f /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.fai /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -f /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.fai /tmp/TNe9AYj4ek/reheader.2.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -f /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.fai /tmp/TNe9AYj4ek/reheader.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.2.hdr -f /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.fai /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.2.hdr -f /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.fai /tmp/TNe9AYj4ek/reheader.2.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools reheader -h /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.2.hdr -f /build/bcftools-L9x9Cm/bcftools-1.13/test/reheader.fai /tmp/TNe9AYj4ek/reheader.2.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view --no-version .. ok test_rename_chrs: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate --rename-chrs /tmp/TNe9AYj4ek/rename.map -Ov /tmp/TNe9AYj4ek/annotate.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate --rename-chrs /tmp/TNe9AYj4ek/rename.map -Ob /tmp/TNe9AYj4ek/annotate.bcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate --rename-chrs /tmp/TNe9AYj4ek/rename.map -Ov /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools annotate --rename-chrs /tmp/TNe9AYj4ek/rename.map -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/annotate.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g -,. /tmp/TNe9AYj4ek/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/convert.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g -,. .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g .,- /tmp/TNe9AYj4ek/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/convert.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g .,- .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g -,. --tag PL /tmp/TNe9AYj4ek/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/convert.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g .,- --tag PL /tmp/TNe9AYj4ek/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/convert.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g -,. --vcf-ids /tmp/TNe9AYj4ek/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/check.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g .,- --vcf-ids /tmp/TNe9AYj4ek/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/check.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g -,. --chrom /tmp/TNe9AYj4ek/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/check.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g -,. --chrom .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g .,- --chrom /tmp/TNe9AYj4ek/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/check.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g .,- --chrom .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g -,. --chrom --vcf-ids /tmp/TNe9AYj4ek/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/check.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g -,. --chrom --vcf-ids .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g .,- --chrom --vcf-ids /tmp/TNe9AYj4ek/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/check.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -g .,- --chrom --vcf-ids .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -h -,.,. /tmp/TNe9AYj4ek/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/convert.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -h .,-,. /tmp/TNe9AYj4ek/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/convert.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -h .,.,- /tmp/TNe9AYj4ek/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/convert.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -H /build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hls.gt.hap,/build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hls.gt.legend,/build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -H /build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hls.gt.hap,/build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hls.gt.legend,/build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hls.gt.samples -Ou | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --vcf-ids -H /build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hls.gt.hap,/build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hls.gt.legend,/build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --vcf-ids -H /build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hls.gt.hap,/build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hls.gt.legend,/build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hls.gt.samples -Ou | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --hapsample2vcf /build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hs.gt.hap,/build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --hapsample2vcf /build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hs.gt.hap,/build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hs.gt.samples -Ou | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hs.gt.hap,/build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hs.gt.hap,/build/bcftools-L9x9Cm/bcftools-1.13/test/convert.hs.gt.samples -Ou | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --hapsample -,. /tmp/TNe9AYj4ek/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/convert.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --hapsample .,- /tmp/TNe9AYj4ek/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/convert.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --hapsample .,- .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --haplegendsample -,.,. /tmp/TNe9AYj4ek/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/convert.hap-missing.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert_gvcf: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa /tmp/TNe9AYj4ek/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view -Ob /tmp/TNe9AYj4ek/convert.gvcf.vcf.gz | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-L9x9Cm/bcftools-1.13/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/23andme.fa --tsv2vcf /build/bcftools-L9x9Cm/bcftools-1.13/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/23andme.fa --tsv2vcf /build/bcftools-L9x9Cm/bcftools-1.13/test/convert.23andme | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -m /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -m /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.tab -c /tmp/TNe9AYj4ek/consensus.1.chain.new >/dev/null; cat /tmp/TNe9AYj4ek/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -H 1 -m /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -H 1 -m /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.tab -c /tmp/TNe9AYj4ek/consensus.2.chain.new >/dev/null; cat /tmp/TNe9AYj4ek/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -I -m /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -I -m /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.tab --mask-with X -m /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -I -m /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.tab -c /tmp/TNe9AYj4ek/consensus.3.chain.new >/dev/null; cat /tmp/TNe9AYj4ek/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -H 1 -c /tmp/TNe9AYj4ek/consensus.4.chain.new >/dev/null; cat /tmp/TNe9AYj4ek/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus2.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus2.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/empty.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus3.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus3.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus4.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus2.fa .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus5.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus6.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus6.fa .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus7.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus7.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus7.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus7.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus8.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus8.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -a . .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus8.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus8.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus8.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus8.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.9.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.9.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.10.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.10.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.11.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.11.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.12.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.12.fa .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.13.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.13.fa .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.14.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.14.fa .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.12.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.12.fa --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.15.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.16.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -I .. ok test_vcf_consensus: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools consensus /tmp/TNe9AYj4ek/consensus.16.vcf.gz -f /build/bcftools-L9x9Cm/bcftools-1.13/test/consensus.fa -H I .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -b /tmp/TNe9AYj4ek/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob -b /tmp/TNe9AYj4ek/mpileup.bam.urllist | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -b /tmp/TNe9AYj4ek/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob -b /tmp/TNe9AYj4ek/mpileup.cram.urllist | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/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-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/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-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/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-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/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-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -S ^/build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -S ^/build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -S ^/build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -r17:100-150 -S ^/build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -t17:100-150 -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.9.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -t17:100-150 -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.9.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -t17:100-150 -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.9.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -t17:100-150 -S /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.9.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -t17:100-150 -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.10.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -t17:100-150 -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.10.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -t17:100-150 -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.10.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -t17:100-150 -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.10.samples -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.1.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.2.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -s HG00102 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -s HG00102 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -s HG00102 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -s HG00102 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -s ^HG99999 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -s ^HG99999 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -s ^HG99999 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -s ^HG99999 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.11.rgs -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.11.rgs -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.11.rgs -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.11.rgs -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.11.rgs -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.11.rgs -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.bam /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.11.rgs -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -G /build/bcftools-L9x9Cm/bcftools-1.13/test/mplp.11.rgs -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.3.cram /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup.4.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.1.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.1.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.1.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.1.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/indel-AD.2.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup-SCR.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup-SCR.bam | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup-SCR.fa /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-L9x9Cm/bcftools-1.13/test/mpileup/mpileup-SCR.cram | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq.gff3 /build/bcftools-L9x9Cm/bcftools-1.13/test/csq.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq.chr.gff3 /build/bcftools-L9x9Cm/bcftools-1.13/test/csq.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq.2.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq.2.gff --ncsq 64 /build/bcftools-L9x9Cm/bcftools-1.13/test/csq.2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EDUMMY0002/EDUMMY0002.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EDUMMY0002/boundaries.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EDUMMY0003/EDUMMY0003.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EDUMMY0003/long-del.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EMN908947 && /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/EMN908947 && /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENSG00000173376/ENSG00000173376.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENSG00000173376/synon.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENSMUST00000121418 && /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENSMUST00000121418 && /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENSMUST00000121418 && /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENSMUST00000133836 && /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000218032/start-lost-del.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000227471/ENST00000227471.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000227471/ENST00000227471.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000230048/ENST00000230048.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000230048/ENST00000230048.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000230048/start-del.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000256452/ENST00000256452.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000256452/ENST00000256452.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000256452/intron.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000263103-INS/insertions.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000271583/ENST00000271583.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000271583/ENST00000271583.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000271583/splice-acceptor.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000301246/ENST00000301246.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000301246/ENST00000301246.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000301246/15bp-insert.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000357367/ENST00000357367.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000357367/ENST00000357367.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000357367/stop-retained.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000368801.2/start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000368801/ENST00000368801.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000368801/ENST00000368801.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000368801/compound-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000375992/ENST00000375992.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000375992/ENST00000375992.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000381157/ENST00000381157.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000381157/ENST00000381157.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000381157/haploid-diploid.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000382647/ENST00000382647.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000382647/ENST00000382647.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000390520/ENST00000390520.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000390520/ENST00000390520.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000390520/deletion-overlap.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000400151/ENST00000400151.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000400151/ENST00000400151.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000400151/long-del.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000409523/ENST00000409523.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000409523/ENST00000409523.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000410009 && /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000410009 && /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000410009 && /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000410009/ENST00000410009.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000410009/ENST00000410009.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000410009/frameshift.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000413103/ENST00000413103.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000413103/ENST00000413103.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000413103/long-deletion.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000420190/ENST00000420190.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000420190/ENST00000420190.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000420670/segfault.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000420670/start-stop-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000423372/snps.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000423372/snps.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000436063/ENST00000436063.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000436063/ENST00000436063.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000436063/insert-before-utr.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000448695/ENST00000448695.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000448695/ENST00000448695.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000518414/ENST00000518414.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000518414/ENST00000518414.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000519442/ENST00000519442.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000519442/ENST00000519442.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000520868/ENST00000520868.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000520868/ENST00000520868.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000520868/long-deletion.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000528237/ENST00000528237.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000528237/ENST00000528237.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000545279/ENST00000545279.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000545279/ENST00000545279.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000545279/splice-region-insert.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000557788/ENST00000557788.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000557788/ENST00000557788.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000557788/long-overlap-del.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -l -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000593942/ENST00000593942.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000593942/ENST00000593942.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools csq -f /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000624631/ENST00000624631.fa -g /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000624631/ENST00000624631.gff /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/ENST00000624631/ambiguous.vcf | /build/bcftools-L9x9Cm/bcftools-1.13/test/csq/sort-csq | /build/bcftools-L9x9Cm/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools roh /build/bcftools-L9x9Cm/bcftools-1.13/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools roh /build/bcftools-L9x9Cm/bcftools-1.13/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-L9x9Cm/bcftools-1.13/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools roh /build/bcftools-L9x9Cm/bcftools-1.13/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-L9x9Cm/bcftools-1.13/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools roh /build/bcftools-L9x9Cm/bcftools-1.13/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools roh /build/bcftools-L9x9Cm/bcftools-1.13/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools roh /build/bcftools-L9x9Cm/bcftools-1.13/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools roh /build/bcftools-L9x9Cm/bcftools-1.13/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 /tmp/TNe9AYj4ek/gtcheck.1.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -u GT,GT /tmp/TNe9AYj4ek/gtcheck.1.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -u GT,PL /tmp/TNe9AYj4ek/gtcheck.1.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -u PL,GT /tmp/TNe9AYj4ek/gtcheck.1.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -u PL,PL /tmp/TNe9AYj4ek/gtcheck.1.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -p s1,s1 /tmp/TNe9AYj4ek/gtcheck.1.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 /tmp/TNe9AYj4ek/gtcheck.2.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 /tmp/TNe9AYj4ek/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/TNe9AYj4ek/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -P /build/bcftools-L9x9Cm/bcftools-1.13/test/gtcheck.3.pairs /tmp/TNe9AYj4ek/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -u PL /tmp/TNe9AYj4ek/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 --n-matches 4 /tmp/TNe9AYj4ek/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/TNe9AYj4ek/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/TNe9AYj4ek/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/TNe9AYj4ek/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/TNe9AYj4ek/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/TNe9AYj4ek/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -p B,C,B,D /tmp/TNe9AYj4ek/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -u GT,GT -H /tmp/TNe9AYj4ek/gtcheck.1.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -u GT,PL -H /tmp/TNe9AYj4ek/gtcheck.1.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -u PL,GT -H /tmp/TNe9AYj4ek/gtcheck.1.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -u PL,PL -H /tmp/TNe9AYj4ek/gtcheck.1.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -P /build/bcftools-L9x9Cm/bcftools-1.13/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/TNe9AYj4ek/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -e 0 -P /build/bcftools-L9x9Cm/bcftools-1.13/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/TNe9AYj4ek/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -u GT -e 30 /tmp/TNe9AYj4ek/gtcheck.1.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/TNe9AYj4ek/gtcheck.1.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -u GT -e 300 /tmp/TNe9AYj4ek/gtcheck.1.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck -u PL -e 30 /tmp/TNe9AYj4ek/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck /tmp/TNe9AYj4ek/gtcheck.ntop.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck --n-matches 2 /tmp/TNe9AYj4ek/gtcheck.ntop.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-L9x9Cm/bcftools-1.13/bcftools gtcheck /tmp/TNe9AYj4ek/gtcheck.5.vcf.gz -g /tmp/TNe9AYj4ek/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok Number of tests: total .. 1285 passed .. 1285 failed .. 0 make[2]: Leaving directory '/build/bcftools-L9x9Cm/bcftools-1.13' make[1]: Leaving directory '/build/bcftools-L9x9Cm/bcftools-1.13' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a make -j12 install DESTDIR=/build/bcftools-L9x9Cm/bcftools-1.13/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/bcftools-L9x9Cm/bcftools-1.13' mkdir -p -m 755 /build/bcftools-L9x9Cm/bcftools-1.13/debian/bcftools/usr/bin /build/bcftools-L9x9Cm/bcftools-1.13/debian/bcftools/usr/share/man/man1 /build/bcftools-L9x9Cm/bcftools-1.13/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /build/bcftools-L9x9Cm/bcftools-1.13/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /build/bcftools-L9x9Cm/bcftools-1.13/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/bcftools-L9x9Cm/bcftools-1.13/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/bcftools-L9x9Cm/bcftools-1.13/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools make[1]: Leaving directory '/build/bcftools-L9x9Cm/bcftools-1.13' debian/rules override_dh_install make[1]: Entering directory '/build/bcftools-L9x9Cm/bcftools-1.13' 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-L9x9Cm/bcftools-1.13' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/build/bcftools-L9x9Cm/bcftools-1.13' dh_installman --language=C make[1]: Leaving directory '/build/bcftools-L9x9Cm/bcftools-1.13' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.13-1_amd64.deb'. dpkg-deb: building package 'bcftools' in '../bcftools_1.13-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../bcftools_1.13-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/bcftools-L9x9Cm /tmp/bcftools-1.13-154vetjdw I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.LzPNBxJKvK... I: success in 2121.4283 seconds md5: bcftools-dbgsym_1.13-1_amd64.deb: OK md5: bcftools_1.13-1_amd64.deb: OK sha1: bcftools-dbgsym_1.13-1_amd64.deb: OK sha1: bcftools_1.13-1_amd64.deb: OK sha256: bcftools-dbgsym_1.13-1_amd64.deb: OK sha256: bcftools_1.13-1_amd64.deb: OK Checksums: OK