Mock Version: 3.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/bcftools.spec'], chrootPath='/var/lib/mock/fedora-rawhide-i686-1672227826.143274/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fb5cxqh9:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fb5cxqh9:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'f22131cec8f8430b8f46db619533a8c9', '-D', '/var/lib/mock/fedora-rawhide-i686-1672227826.143274/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fb5cxqh9:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/bcftools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1661212800 Wrote: /builddir/build/SRPMS/bcftools-1.15.1-2.fc38.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/bcftools.spec'], chrootPath='/var/lib/mock/fedora-rawhide-i686-1672227826.143274/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fb5cxqh9:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fb5cxqh9:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '00c5fa949fa647d38a29b2ffafe0906c', '-D', '/var/lib/mock/fedora-rawhide-i686-1672227826.143274/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fb5cxqh9:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/bcftools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1661212800 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.q9A9DT + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bcftools-1.15.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/bcftools-1.15.1.tar.bz2 + STATUS=0 + '[' 0 -ne 0 ']' + cd bcftools-1.15.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (bcftools-1.15.1-aarch64-fix-vcf_plugin-tests.patch): + echo 'Patch #0 (bcftools-1.15.1-aarch64-fix-vcf_plugin-tests.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file plugins/fill-tags.c + sed -i '1s|/usr/bin/env perl|/usr/bin/perl|' misc/color-chrs.pl misc/demo-flt.pl misc/run-roh.pl misc/vcfutils.pl misc/plot-vcfstats + sed -i '1s|/usr/bin/env python3\{0,1\}|/usr/bin/python3|' misc/gff2gff.py misc/guess-ploidy.py misc/plot-roh.py + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.nMXnSQ + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bcftools-1.15.1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure --- ./htslib-1.15.1/configure.backup 2022-04-07 15:42:52.000000000 +0000 +++ ./htslib-1.15.1/configure 2022-12-28 11:44:53.035583106 +0000 @@ -1697,7 +1697,7 @@ #ifdef __cplusplus extern "C" #endif -char $2 (); +__attribute__ ((used)) char $2 (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.15.1/configure + diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=i686-redhat-linux-gnu --host=i686-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' --prefix=/usr --with-htslib=system --enable-perl-filters --enable-libgsl '--with-bcf-plugin-path=/usr/local/libexec/bcftools:$(plugindir)' checking for i686-redhat-linux-gnu-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for gsl/gsl_version.h... yes checking for library containing cblas_dgemm... -lgslcblas checking for gsl_multifit_gradient in -lgsl... yes checking for library containing Perl_call_pv... -lperl checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h configure: License has been changed to GPL. Linking against the GNU scientific library requires that the resulting binary is licensed using the GNU General Public License. In particular, this means you will have to follow the terms of this license in order to distribute binary copies. For more information see the INSTALL file. Text of the GNU General Public License can be found in the LICENSE file, or at http://www.gnu.org/copyleft/gpl.html Information on the GNU Scientific Library, including the rationale for its choice of license can be found at https://www.gnu.org/software/gsl/ + /usr/bin/make -O -j2 V=1 VERBOSE=1 echo '#define BCFTOOLS_VERSION "1.15.1"' > version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o tabix.o tabix.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfindex.o vcfindex.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfisec.o vcfisec.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfstats.o vcfstats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfquery.o vcfquery.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcffilter.o vcffilter.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfmerge.o vcfmerge.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfsom.o vcfsom.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/perl5/CORE -c -o filter.o filter.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches 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-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfview.o vcfview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfroh.o vcfroh.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfconcat.o vcfconcat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfannotate.o vcfannotate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfcall.o vcfcall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcmp.o vcmp.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o gvcf.o gvcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o mcall.o mcall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o reheader.o reheader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfconvert.o vcfconvert.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o tsv2vcf.o tsv2vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o convert.o convert.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfhead.o vcfhead.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfcnv.o vcfcnv.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o HMM.o HMM.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o ploidy.o ploidy.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o bin.o bin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o consensus.o consensus.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o hclust.o hclust.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o version.o version.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o smpl_ilist.o smpl_ilist.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfbuf.o vcfbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o mpileup.o mpileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o bam2bcf.o bam2bcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o csq.o csq.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o vcfsort.o vcfsort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o cols.o cols.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o extsort.o extsort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o bam_sample.o bam_sample.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o dist.o dist.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o ccall.o ccall.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o em.o em.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o abuf.o abuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o kmin.o kmin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o str_finder.o str_finder.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o prob1.o prob1.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o peakfit.o peakfit.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o polysomy.o polysomy.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o test/test-rbuf.o test/test-rbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -DPLUGINPATH='"/usr/local/libexec/bcftools:/usr/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 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-specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches 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gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/mendelian.so version.c plugins/mendelian.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 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-specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall 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-mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -DUSE_GPL -c -o main.o main.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/test-rbuf test/test-rbuf.o -lz gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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 vcfhead.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 polysomy.o peakfit.o vcfplugin.o -lhts -lm -lz -lgsl -lgslcblas -Wl,--enable-new-dtags -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -fstack-protector-strong -L/usr/local/lib -L/usr/lib/perl5/CORE -lperl -lpthread -lresolv -ldl -lm -lcrypt -lutil -lc -lpthread + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.l4aPdq + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386 ++ dirname /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bcftools-1.15.1 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/bin /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/share/man/man1 /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools /usr/bin/install -p bcftools /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/bin /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 /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/bin /usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/share/man/man1 /usr/bin/install -p plugins/*.so /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.15.1-2.fc38 --unique-debug-suffix -1.15.1-2.fc38.i386 --unique-debug-src-base bcftools-1.15.1-2.fc38.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bcftools-1.15.1 extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/bin/bcftools extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/GTisec.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/GTsubset.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/ad-bias.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/add-variantkey.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/af-dist.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/allele-length.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/check-ploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/check-sparsity.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/color-chrs.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/contrast.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/counts.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/dosage.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/fill-AN-AC.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/fill-from-fasta.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/fill-tags.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/fixref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/fixploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/frameshifts.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/guess-ploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/gvcfz.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/impute-info.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/indel-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/isecGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/mendelian.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/missing2ref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/parental-origin.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/prune.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/remove-overlaps.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/scatter.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/setGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/smpl-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/split-vep.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/split.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/tag2tag.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/trio-dnm2.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/trio-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/trio-switch-rate.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/libexec/bcftools/variantkey-hex.so original debug info size: 5604kB, size after compression: 4844kB /usr/bin/sepdebugcrcfix: Updated 39 CRC32s, 0 CRC32s did match. 5400 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.ZOAwGb + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bcftools-1.15.1 + ldd bcftools + grep -E '/lib(64)?/libhts\.so\.' libhts.so.3 => /lib/libhts.so.3 (0xf7d9b000) + sed -i -E '/^test_vcf_convert_hs2vcf.+convert.gs.gt.ids.3N6.gen.+/ s/^/#/' test/test.pl + make test ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools ./test/test.pl: module IO::Pty not found; skipping usage tests test_tabix: tabix /tmp/g8Is9I9_Su/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/g8Is9I9_Su/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/g8Is9I9_Su/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/g8Is9I9_Su/merge.a.bcf 1:3000151-3000151 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/g8Is9I9_Su/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/g8Is9I9_Su/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/g8Is9I9_Su/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/g8Is9I9_Su/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/g8Is9I9_Su/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/g8Is9I9_Su/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/g8Is9I9_Su/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/g8Is9I9_Su/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/g8Is9I9_Su/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H /tmp/g8Is9I9_Su/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -s /tmp/g8Is9I9_Su/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -s /tmp/g8Is9I9_Su/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -s /tmp/g8Is9I9_Su/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/g8Is9I9_Su/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/g8Is9I9_Su/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/g8Is9I9_Su/idx.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/g8Is9I9_Su/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/g8Is9I9_Su/idx.bcf.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -s /tmp/g8Is9I9_Su/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -s /tmp/g8Is9I9_Su/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -s /tmp/g8Is9I9_Su/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/g8Is9I9_Su/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/g8Is9I9_Su/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/g8Is9I9_Su/empty.vcf.gz.csi .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/g8Is9I9_Su/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.15.1/bcftools index -n /tmp/g8Is9I9_Su/empty.bcf.csi .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.15.1/bcftools stats -s - /tmp/g8Is9I9_Su/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /builddir/build/BUILD/bcftools-1.15.1/misc/plot-vcfstats -m /tmp/g8Is9I9_Su/check.1.chk /tmp/g8Is9I9_Su/check.2.chk /tmp/g8Is9I9_Su/check.3.chk /tmp/g8Is9I9_Su/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.15.1/bcftools stats -s - /tmp/g8Is9I9_Su/stats.a.vcf.gz /tmp/g8Is9I9_Su/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.15.1/bcftools stats -s B /tmp/g8Is9I9_Su/stats.a.vcf.gz /tmp/g8Is9I9_Su/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.15.1/bcftools stats -s - /tmp/g8Is9I9_Su/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -n =2 /tmp/g8Is9I9_Su/isec.a.vcf.gz /tmp/g8Is9I9_Su/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -n =2 /tmp/g8Is9I9_Su/isec.a.vcf.gz /tmp/g8Is9I9_Su/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/g8Is9I9_Su/isec.a.vcf.gz /tmp/g8Is9I9_Su/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/g8Is9I9_Su/isec.a.vcf.gz /tmp/g8Is9I9_Su/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -n =2 -c both /tmp/g8Is9I9_Su/isec.a.vcf.gz /tmp/g8Is9I9_Su/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -n =2 -c both /tmp/g8Is9I9_Su/isec.a.vcf.gz /tmp/g8Is9I9_Su/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -n =2 -c any /tmp/g8Is9I9_Su/isec.a.vcf.gz /tmp/g8Is9I9_Su/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -n =2 -c any /tmp/g8Is9I9_Su/isec.a.vcf.gz /tmp/g8Is9I9_Su/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -C -c any /tmp/g8Is9I9_Su/isec.a.vcf.gz /tmp/g8Is9I9_Su/isec.b.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -C -c any /tmp/g8Is9I9_Su/isec.a.vcf.gz /tmp/g8Is9I9_Su/isec.b.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec --no-version -T /tmp/g8Is9I9_Su/isec.tab.gz /tmp/g8Is9I9_Su/isec.a.vcf.gz .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -T /tmp/g8Is9I9_Su/isec.tab.gz /tmp/g8Is9I9_Su/isec.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/g8Is9I9_Su/isec-miss.1.1.vcf.gz /tmp/g8Is9I9_Su/isec-miss.1.2.vcf.gz /tmp/g8Is9I9_Su/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/g8Is9I9_Su/isec-miss.1.1.vcf.gz /tmp/g8Is9I9_Su/isec-miss.1.2.vcf.gz /tmp/g8Is9I9_Su/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -R /builddir/build/BUILD/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/g8Is9I9_Su/isec-miss.1.1.vcf.gz /tmp/g8Is9I9_Su/isec-miss.1.2.vcf.gz /tmp/g8Is9I9_Su/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/g8Is9I9_Su/isec-miss.1.1.vcf.gz /tmp/g8Is9I9_Su/isec-miss.1.2.vcf.gz /tmp/g8Is9I9_Su/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/g8Is9I9_Su/isec-miss.2.1.vcf.gz /tmp/g8Is9I9_Su/isec-miss.2.2.vcf.gz /tmp/g8Is9I9_Su/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/g8Is9I9_Su/isec-miss.2.1.vcf.gz /tmp/g8Is9I9_Su/isec-miss.2.2.vcf.gz /tmp/g8Is9I9_Su/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -R /builddir/build/BUILD/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/g8Is9I9_Su/isec-miss.2.1.vcf.gz /tmp/g8Is9I9_Su/isec-miss.2.2.vcf.gz /tmp/g8Is9I9_Su/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.15.1/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.15.1/test/isec-miss.1.regs.txt -n +1 /tmp/g8Is9I9_Su/isec-miss.2.1.vcf.gz /tmp/g8Is9I9_Su/isec-miss.2.2.vcf.gz /tmp/g8Is9I9_Su/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -i AF:join /tmp/g8Is9I9_Su/merge.join.a.vcf.gz /tmp/g8Is9I9_Su/merge.join.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -i AF:join /tmp/g8Is9I9_Su/merge.join.a.vcf.gz /tmp/g8Is9I9_Su/merge.join.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -i AF:join /tmp/g8Is9I9_Su/merge.join.a.bcf /tmp/g8Is9I9_Su/merge.join.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -i AF:join /tmp/g8Is9I9_Su/merge.join.a.bcf /tmp/g8Is9I9_Su/merge.join.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/g8Is9I9_Su/merge.LPL.a.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.b.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/g8Is9I9_Su/merge.LPL.a.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.b.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/g8Is9I9_Su/merge.LPL.a.bcf /tmp/g8Is9I9_Su/merge.LPL.b.bcf /tmp/g8Is9I9_Su/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/g8Is9I9_Su/merge.LPL.a.bcf /tmp/g8Is9I9_Su/merge.LPL.b.bcf /tmp/g8Is9I9_Su/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 1 /tmp/g8Is9I9_Su/merge.LPL.a.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.b.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 1 /tmp/g8Is9I9_Su/merge.LPL.a.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.b.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 1 /tmp/g8Is9I9_Su/merge.LPL.a.bcf /tmp/g8Is9I9_Su/merge.LPL.b.bcf /tmp/g8Is9I9_Su/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 1 /tmp/g8Is9I9_Su/merge.LPL.a.bcf /tmp/g8Is9I9_Su/merge.LPL.b.bcf /tmp/g8Is9I9_Su/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 2 /tmp/g8Is9I9_Su/merge.LPL.a.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.b.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 2 /tmp/g8Is9I9_Su/merge.LPL.a.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.b.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 2 /tmp/g8Is9I9_Su/merge.LPL.a.bcf /tmp/g8Is9I9_Su/merge.LPL.b.bcf /tmp/g8Is9I9_Su/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 2 /tmp/g8Is9I9_Su/merge.LPL.a.bcf /tmp/g8Is9I9_Su/merge.LPL.b.bcf /tmp/g8Is9I9_Su/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 3 /tmp/g8Is9I9_Su/merge.LPL.a.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.b.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 3 /tmp/g8Is9I9_Su/merge.LPL.a.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.b.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 3 /tmp/g8Is9I9_Su/merge.LPL.a.bcf /tmp/g8Is9I9_Su/merge.LPL.b.bcf /tmp/g8Is9I9_Su/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 3 /tmp/g8Is9I9_Su/merge.LPL.a.bcf /tmp/g8Is9I9_Su/merge.LPL.b.bcf /tmp/g8Is9I9_Su/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 4 /tmp/g8Is9I9_Su/merge.LPL.a.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.b.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 4 /tmp/g8Is9I9_Su/merge.LPL.a.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.b.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 4 /tmp/g8Is9I9_Su/merge.LPL.a.bcf /tmp/g8Is9I9_Su/merge.LPL.b.bcf /tmp/g8Is9I9_Su/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 4 /tmp/g8Is9I9_Su/merge.LPL.a.bcf /tmp/g8Is9I9_Su/merge.LPL.b.bcf /tmp/g8Is9I9_Su/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 5 /tmp/g8Is9I9_Su/merge.LPL.a.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.b.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 5 /tmp/g8Is9I9_Su/merge.LPL.a.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.b.vcf.gz /tmp/g8Is9I9_Su/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -L 5 /tmp/g8Is9I9_Su/merge.LPL.a.bcf /tmp/g8Is9I9_Su/merge.LPL.b.bcf /tmp/g8Is9I9_Su/merge.LPL.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -L 5 /tmp/g8Is9I9_Su/merge.LPL.a.bcf /tmp/g8Is9I9_Su/merge.LPL.b.bcf /tmp/g8Is9I9_Su/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/g8Is9I9_Su/merge.a.vcf.gz /tmp/g8Is9I9_Su/merge.b.vcf.gz /tmp/g8Is9I9_Su/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/g8Is9I9_Su/merge.a.vcf.gz /tmp/g8Is9I9_Su/merge.b.vcf.gz /tmp/g8Is9I9_Su/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/g8Is9I9_Su/merge.a.bcf /tmp/g8Is9I9_Su/merge.b.bcf /tmp/g8Is9I9_Su/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/g8Is9I9_Su/merge.a.bcf /tmp/g8Is9I9_Su/merge.b.bcf /tmp/g8Is9I9_Su/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -Fx /tmp/g8Is9I9_Su/merge.a.vcf.gz /tmp/g8Is9I9_Su/merge.b.vcf.gz /tmp/g8Is9I9_Su/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -Fx /tmp/g8Is9I9_Su/merge.a.vcf.gz /tmp/g8Is9I9_Su/merge.b.vcf.gz /tmp/g8Is9I9_Su/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -Fx /tmp/g8Is9I9_Su/merge.a.bcf /tmp/g8Is9I9_Su/merge.b.bcf /tmp/g8Is9I9_Su/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -Fx /tmp/g8Is9I9_Su/merge.a.bcf /tmp/g8Is9I9_Su/merge.b.bcf /tmp/g8Is9I9_Su/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -0 /tmp/g8Is9I9_Su/merge.a.vcf.gz /tmp/g8Is9I9_Su/merge.b.vcf.gz /tmp/g8Is9I9_Su/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -0 /tmp/g8Is9I9_Su/merge.a.vcf.gz /tmp/g8Is9I9_Su/merge.b.vcf.gz /tmp/g8Is9I9_Su/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -0 /tmp/g8Is9I9_Su/merge.a.bcf /tmp/g8Is9I9_Su/merge.b.bcf /tmp/g8Is9I9_Su/merge.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -0 /tmp/g8Is9I9_Su/merge.a.bcf /tmp/g8Is9I9_Su/merge.b.bcf /tmp/g8Is9I9_Su/merge.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m none /tmp/g8Is9I9_Su/merge.2.a.vcf.gz /tmp/g8Is9I9_Su/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m none /tmp/g8Is9I9_Su/merge.2.a.vcf.gz /tmp/g8Is9I9_Su/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m none /tmp/g8Is9I9_Su/merge.2.a.bcf /tmp/g8Is9I9_Su/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m none /tmp/g8Is9I9_Su/merge.2.a.bcf /tmp/g8Is9I9_Su/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m both /tmp/g8Is9I9_Su/merge.2.a.vcf.gz /tmp/g8Is9I9_Su/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m both /tmp/g8Is9I9_Su/merge.2.a.vcf.gz /tmp/g8Is9I9_Su/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m both /tmp/g8Is9I9_Su/merge.2.a.bcf /tmp/g8Is9I9_Su/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m both /tmp/g8Is9I9_Su/merge.2.a.bcf /tmp/g8Is9I9_Su/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m all /tmp/g8Is9I9_Su/merge.2.a.vcf.gz /tmp/g8Is9I9_Su/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m all /tmp/g8Is9I9_Su/merge.2.a.vcf.gz /tmp/g8Is9I9_Su/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m all /tmp/g8Is9I9_Su/merge.2.a.bcf /tmp/g8Is9I9_Su/merge.2.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m all /tmp/g8Is9I9_Su/merge.2.a.bcf /tmp/g8Is9I9_Su/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/g8Is9I9_Su/merge.3.a.vcf.gz /tmp/g8Is9I9_Su/merge.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/g8Is9I9_Su/merge.3.a.vcf.gz /tmp/g8Is9I9_Su/merge.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/g8Is9I9_Su/merge.3.a.bcf /tmp/g8Is9I9_Su/merge.3.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/g8Is9I9_Su/merge.3.a.bcf /tmp/g8Is9I9_Su/merge.3.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m id /tmp/g8Is9I9_Su/merge.4.a.vcf.gz /tmp/g8Is9I9_Su/merge.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m id /tmp/g8Is9I9_Su/merge.4.a.vcf.gz /tmp/g8Is9I9_Su/merge.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples -m id /tmp/g8Is9I9_Su/merge.4.a.bcf /tmp/g8Is9I9_Su/merge.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples -m id /tmp/g8Is9I9_Su/merge.4.a.bcf /tmp/g8Is9I9_Su/merge.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/g8Is9I9_Su/gvcf.merge.1.vcf.gz /tmp/g8Is9I9_Su/gvcf.merge.2.vcf.gz /tmp/g8Is9I9_Su/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/g8Is9I9_Su/gvcf.merge.1.vcf.gz /tmp/g8Is9I9_Su/gvcf.merge.2.vcf.gz /tmp/g8Is9I9_Su/gvcf.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/g8Is9I9_Su/gvcf.merge.1.bcf /tmp/g8Is9I9_Su/gvcf.merge.2.bcf /tmp/g8Is9I9_Su/gvcf.merge.3.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/g8Is9I9_Su/gvcf.merge.1.bcf /tmp/g8Is9I9_Su/gvcf.merge.2.bcf /tmp/g8Is9I9_Su/gvcf.merge.3.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.2.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.2.b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.2.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.2.b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - -i SRC:join /tmp/g8Is9I9_Su/merge.gvcf.3.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - -i SRC:join /tmp/g8Is9I9_Su/merge.gvcf.3.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.4.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.4.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.4.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.4.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/g8Is9I9_Su/merge.5.a.vcf.gz /tmp/g8Is9I9_Su/merge.5.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/g8Is9I9_Su/merge.5.a.vcf.gz /tmp/g8Is9I9_Su/merge.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/g8Is9I9_Su/merge.5.a.bcf /tmp/g8Is9I9_Su/merge.5.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/g8Is9I9_Su/merge.5.a.bcf /tmp/g8Is9I9_Su/merge.5.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/g8Is9I9_Su/merge.6.a.vcf.gz /tmp/g8Is9I9_Su/merge.6.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/g8Is9I9_Su/merge.6.a.vcf.gz /tmp/g8Is9I9_Su/merge.6.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/g8Is9I9_Su/merge.6.a.bcf /tmp/g8Is9I9_Su/merge.6.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/g8Is9I9_Su/merge.6.a.bcf /tmp/g8Is9I9_Su/merge.6.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.7.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.7.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.7.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.7.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.7.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.8.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.8.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.8.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf - /tmp/g8Is9I9_Su/merge.gvcf.8.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/g8Is9I9_Su/merge.7.a.vcf.gz /tmp/g8Is9I9_Su/merge.7.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/g8Is9I9_Su/merge.7.a.vcf.gz /tmp/g8Is9I9_Su/merge.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --force-samples /tmp/g8Is9I9_Su/merge.7.a.bcf /tmp/g8Is9I9_Su/merge.7.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --force-samples /tmp/g8Is9I9_Su/merge.7.a.bcf /tmp/g8Is9I9_Su/merge.7.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/g8Is9I9_Su/merge.gvcf.9a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9c.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/g8Is9I9_Su/merge.gvcf.9a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9c.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/g8Is9I9_Su/merge.gvcf.9a.bcf /tmp/g8Is9I9_Su/merge.gvcf.9b.bcf /tmp/g8Is9I9_Su/merge.gvcf.9c.bcf /tmp/g8Is9I9_Su/merge.gvcf.9d.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/g8Is9I9_Su/merge.gvcf.9a.bcf /tmp/g8Is9I9_Su/merge.gvcf.9b.bcf /tmp/g8Is9I9_Su/merge.gvcf.9c.bcf /tmp/g8Is9I9_Su/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/g8Is9I9_Su/merge.gvcf.9a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9c.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/g8Is9I9_Su/merge.gvcf.9a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9c.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/g8Is9I9_Su/merge.gvcf.9a.bcf /tmp/g8Is9I9_Su/merge.gvcf.9b.bcf /tmp/g8Is9I9_Su/merge.gvcf.9c.bcf /tmp/g8Is9I9_Su/merge.gvcf.9d.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/g8Is9I9_Su/merge.gvcf.9a.bcf /tmp/g8Is9I9_Su/merge.gvcf.9b.bcf /tmp/g8Is9I9_Su/merge.gvcf.9c.bcf /tmp/g8Is9I9_Su/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/g8Is9I9_Su/merge.gvcf.9a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9c.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9d.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/g8Is9I9_Su/merge.gvcf.9a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9c.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9d.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/g8Is9I9_Su/merge.gvcf.9a.bcf /tmp/g8Is9I9_Su/merge.gvcf.9b.bcf /tmp/g8Is9I9_Su/merge.gvcf.9c.bcf /tmp/g8Is9I9_Su/merge.gvcf.9d.bcf /tmp/g8Is9I9_Su/merge.gvcf.9e.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/g8Is9I9_Su/merge.gvcf.9a.bcf /tmp/g8Is9I9_Su/merge.gvcf.9b.bcf /tmp/g8Is9I9_Su/merge.gvcf.9c.bcf /tmp/g8Is9I9_Su/merge.gvcf.9d.bcf /tmp/g8Is9I9_Su/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/g8Is9I9_Su/merge.gvcf.9a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9c.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9d.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/g8Is9I9_Su/merge.gvcf.9a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9c.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9d.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/g8Is9I9_Su/merge.gvcf.9a.bcf /tmp/g8Is9I9_Su/merge.gvcf.9b.bcf /tmp/g8Is9I9_Su/merge.gvcf.9c.bcf /tmp/g8Is9I9_Su/merge.gvcf.9d.bcf /tmp/g8Is9I9_Su/merge.gvcf.9e.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa -r 22:21-23 /tmp/g8Is9I9_Su/merge.gvcf.9a.bcf /tmp/g8Is9I9_Su/merge.gvcf.9b.bcf /tmp/g8Is9I9_Su/merge.gvcf.9c.bcf /tmp/g8Is9I9_Su/merge.gvcf.9d.bcf /tmp/g8Is9I9_Su/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/g8Is9I9_Su/merge.gvcf.10.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/g8Is9I9_Su/merge.gvcf.10.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/g8Is9I9_Su/merge.gvcf.10.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/g8Is9I9_Su/merge.gvcf.10.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -m none /tmp/g8Is9I9_Su/merge.gvcf.10.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -m none /tmp/g8Is9I9_Su/merge.gvcf.10.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -m none /tmp/g8Is9I9_Su/merge.gvcf.10.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -m none /tmp/g8Is9I9_Su/merge.gvcf.10.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/g8Is9I9_Su/merge.gvcf.10.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/g8Is9I9_Su/merge.gvcf.10.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/g8Is9I9_Su/merge.gvcf.10.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/g8Is9I9_Su/merge.gvcf.10.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/g8Is9I9_Su/merge.gvcf.10.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/g8Is9I9_Su/merge.gvcf.10.a.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/g8Is9I9_Su/merge.gvcf.10.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/g8Is9I9_Su/merge.gvcf.10.a.bcf /tmp/g8Is9I9_Su/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/g8Is9I9_Su/merge.gvcf.10.b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/g8Is9I9_Su/merge.gvcf.10.b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/g8Is9I9_Su/merge.gvcf.10.b.bcf /tmp/g8Is9I9_Su/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa /tmp/g8Is9I9_Su/merge.gvcf.10.b.bcf /tmp/g8Is9I9_Su/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/g8Is9I9_Su/merge.gvcf.10.b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/g8Is9I9_Su/merge.gvcf.10.b.vcf.gz /tmp/g8Is9I9_Su/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/g8Is9I9_Su/merge.gvcf.10.b.bcf /tmp/g8Is9I9_Su/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.15.1/test/merge.gvcf.10.fa -m none /tmp/g8Is9I9_Su/merge.gvcf.10.b.bcf /tmp/g8Is9I9_Su/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/g8Is9I9_Su/merge.noidx.a.vcf.gz /tmp/g8Is9I9_Su/merge.noidx.b.vcf.gz /tmp/g8Is9I9_Su/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/g8Is9I9_Su/merge.noidx.a.vcf.gz /tmp/g8Is9I9_Su/merge.noidx.b.vcf.gz /tmp/g8Is9I9_Su/merge.noidx.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/g8Is9I9_Su/merge.noidx.a.bcf /tmp/g8Is9I9_Su/merge.noidx.b.bcf /tmp/g8Is9I9_Su/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/g8Is9I9_Su/merge.noidx.a.bcf /tmp/g8Is9I9_Su/merge.noidx.b.bcf /tmp/g8Is9I9_Su/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --no-index /builddir/build/BUILD/bcftools-1.15.1/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.15.1/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.15.1/test/merge.noidx.c.vcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --no-index /builddir/build/BUILD/bcftools-1.15.1/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.15.1/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.15.1/test/merge.noidx.c.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version --no-index /tmp/g8Is9I9_Su/merge.noidx.a.bcf /tmp/g8Is9I9_Su/merge.noidx.b.bcf /tmp/g8Is9I9_Su/merge.noidx.c.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob --no-index /tmp/g8Is9I9_Su/merge.noidx.a.bcf /tmp/g8Is9I9_Su/merge.noidx.b.bcf /tmp/g8Is9I9_Su/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/g8Is9I9_Su/merge.8.a.vcf.gz /tmp/g8Is9I9_Su/merge.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/g8Is9I9_Su/merge.8.a.vcf.gz /tmp/g8Is9I9_Su/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/g8Is9I9_Su/merge.8.a.bcf /tmp/g8Is9I9_Su/merge.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/g8Is9I9_Su/merge.8.a.bcf /tmp/g8Is9I9_Su/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/g8Is9I9_Su/merge.8.a.vcf.gz /tmp/g8Is9I9_Su/merge.8.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/g8Is9I9_Su/merge.8.a.vcf.gz /tmp/g8Is9I9_Su/merge.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/g8Is9I9_Su/merge.8.a.bcf /tmp/g8Is9I9_Su/merge.8.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/g8Is9I9_Su/merge.8.a.bcf /tmp/g8Is9I9_Su/merge.8.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/g8Is9I9_Su/merge.9.a.vcf.gz /tmp/g8Is9I9_Su/merge.9.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/g8Is9I9_Su/merge.9.a.vcf.gz /tmp/g8Is9I9_Su/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version /tmp/g8Is9I9_Su/merge.9.a.bcf /tmp/g8Is9I9_Su/merge.9.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob /tmp/g8Is9I9_Su/merge.9.a.bcf /tmp/g8Is9I9_Su/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/g8Is9I9_Su/merge.9.a.vcf.gz /tmp/g8Is9I9_Su/merge.9.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/g8Is9I9_Su/merge.9.a.vcf.gz /tmp/g8Is9I9_Su/merge.9.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge --no-version -i AN:sum,AC:sum /tmp/g8Is9I9_Su/merge.9.a.bcf /tmp/g8Is9I9_Su/merge.9.b.bcf .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.15.1/bcftools merge -Ob -i AN:sum,AC:sum /tmp/g8Is9I9_Su/merge.9.a.bcf /tmp/g8Is9I9_Su/merge.9.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/g8Is9I9_Su/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/g8Is9I9_Su/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/g8Is9I9_Su/query.string.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%RSX\t%VKX\n' /tmp/g8Is9I9_Su/query.variantkey.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.variantkey.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/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/g8Is9I9_Su/view.vectors.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/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: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/g8Is9I9_Su/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/g8Is9I9_Su/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/g8Is9I9_Su/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/g8Is9I9_Su/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/g8Is9I9_Su/query.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/g8Is9I9_Su/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/g8Is9I9_Su/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/g8Is9I9_Su/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/g8Is9I9_Su/filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%LINE' /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%LINE' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/g8Is9I9_Su/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/g8Is9I9_Su/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/g8Is9I9_Su/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/g8Is9I9_Su/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/g8Is9I9_Su/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/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/g8Is9I9_Su/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/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: /builddir/build/BUILD/bcftools-1.15.1/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/g8Is9I9_Su/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/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: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/g8Is9I9_Su/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/g8Is9I9_Su/query.filter.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/g8Is9I9_Su/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/g8Is9I9_Su/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/g8Is9I9_Su/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/g8Is9I9_Su/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/g8Is9I9_Su/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/g8Is9I9_Su/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/g8Is9I9_Su/query.filter.4.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.15.1/test/query.56.out' /tmp/g8Is9I9_Su/view.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.15.1/test/query.56.out' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/g8Is9I9_Su/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/g8Is9I9_Su/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/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: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/g8Is9I9_Su/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/g8Is9I9_Su/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/g8Is9I9_Su/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/g8Is9I9_Su/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/g8Is9I9_Su/query.negative.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/g8Is9I9_Su/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/g8Is9I9_Su/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/g8Is9I9_Su/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/g8Is9I9_Su/query.filter.11.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' /tmp/g8Is9I9_Su/query.pbinom.1.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.pbinom.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/g8Is9I9_Su/query.filter.6.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.6.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/g8Is9I9_Su/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/g8Is9I9_Su/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/g8Is9I9_Su/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/g8Is9I9_Su/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/g8Is9I9_Su/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/g8Is9I9_Su/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/g8Is9I9_Su/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/g8Is9I9_Su/query.filter.7.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/g8Is9I9_Su/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/g8Is9I9_Su/query.filter.8.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/g8Is9I9_Su/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/g8Is9I9_Su/query.filter.9.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/g8Is9I9_Su/query.filter.13.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.13.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/g8Is9I9_Su/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/g8Is9I9_Su/query.filter.10.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/g8Is9I9_Su/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/g8Is9I9_Su/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/g8Is9I9_Su/query.filter.12.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt /tmp/g8Is9I9_Su/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt /tmp/g8Is9I9_Su/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt /tmp/g8Is9I9_Su/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S ^/builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt /tmp/g8Is9I9_Su/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l -S ^/builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.11.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.txt /tmp/g8Is9I9_Su/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f "[%SAMPLE %GT\n]" -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.txt /tmp/g8Is9I9_Su/query.smpl.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.smpl.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l -S /builddir/build/BUILD/bcftools-1.15.1/test/query.smpl.txt .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/g8Is9I9_Su/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/g8Is9I9_Su/query.filter.id.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/query.filter.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -cx -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/g8Is9I9_Su/norm.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -cx -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/g8Is9I9_Su/norm.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/g8Is9I9_Su/norm.split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/g8Is9I9_Su/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/g8Is9I9_Su/norm.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/g8Is9I9_Su/norm.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m- --force /tmp/g8Is9I9_Su/norm.split.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m- --force /tmp/g8Is9I9_Su/norm.split.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m- /tmp/g8Is9I9_Su/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m- /tmp/g8Is9I9_Su/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m- --keep-sum AD /tmp/g8Is9I9_Su/norm.split.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m- --keep-sum AD /tmp/g8Is9I9_Su/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/g8Is9I9_Su/norm.split.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/g8Is9I9_Su/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/g8Is9I9_Su/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/g8Is9I9_Su/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/g8Is9I9_Su/norm.merge.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/g8Is9I9_Su/norm.merge.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m+ /tmp/g8Is9I9_Su/norm.merge.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m+ /tmp/g8Is9I9_Su/norm.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m+ -s /tmp/g8Is9I9_Su/norm.merge.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m+ -s /tmp/g8Is9I9_Su/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -Nc s -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/g8Is9I9_Su/norm.setref.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -Nc s -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/g8Is9I9_Su/norm.setref.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/g8Is9I9_Su/norm.telomere.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa /tmp/g8Is9I9_Su/norm.telomere.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d snps /tmp/g8Is9I9_Su/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d snps /tmp/g8Is9I9_Su/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d indels /tmp/g8Is9I9_Su/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d indels /tmp/g8Is9I9_Su/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d both /tmp/g8Is9I9_Su/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d both /tmp/g8Is9I9_Su/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d all /tmp/g8Is9I9_Su/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d all /tmp/g8Is9I9_Su/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d none /tmp/g8Is9I9_Su/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d none /tmp/g8Is9I9_Su/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d exact /tmp/g8Is9I9_Su/norm.rmdup.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d exact /tmp/g8Is9I9_Su/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d none /tmp/g8Is9I9_Su/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d none /tmp/g8Is9I9_Su/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d exact /tmp/g8Is9I9_Su/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d exact /tmp/g8Is9I9_Su/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d indels /tmp/g8Is9I9_Su/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d indels /tmp/g8Is9I9_Su/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d any /tmp/g8Is9I9_Su/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d any /tmp/g8Is9I9_Su/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d both /tmp/g8Is9I9_Su/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d both /tmp/g8Is9I9_Su/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -d snps /tmp/g8Is9I9_Su/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -d snps /tmp/g8Is9I9_Su/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -c s -a -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.2.fa /tmp/g8Is9I9_Su/norm.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -c s -a -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.2.fa /tmp/g8Is9I9_Su/norm.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -c s -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.iupac.fa /tmp/g8Is9I9_Su/norm.iupac.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -c s -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.iupac.fa /tmp/g8Is9I9_Su/norm.iupac.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -c s -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.3.fa /tmp/g8Is9I9_Su/norm.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -c s -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.3.fa /tmp/g8Is9I9_Su/norm.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/g8Is9I9_Su/atomize.split.1.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/g8Is9I9_Su/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/g8Is9I9_Su/atomize.split.1.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/g8Is9I9_Su/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/g8Is9I9_Su/atomize.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/g8Is9I9_Su/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/g8Is9I9_Su/atomize.split.2.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/g8Is9I9_Su/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version --atomize --atom-overlaps . /tmp/g8Is9I9_Su/atomize.split.3.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob --atomize --atom-overlaps . /tmp/g8Is9I9_Su/atomize.split.3.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m +both /tmp/g8Is9I9_Su/norm.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m +both /tmp/g8Is9I9_Su/norm.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm --no-version -m +any /tmp/g8Is9I9_Su/norm.4.vcf.gz .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.15.1/bcftools norm -Ob -m +any /tmp/g8Is9I9_Su/norm.4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/g8Is9I9_Su/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/g8Is9I9_Su/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -f PASS -Xks NA00003 /tmp/g8Is9I9_Su/view.vcf.gz -r20,Y .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -f PASS -Xks NA00003 /tmp/g8Is9I9_Su/view.vcf.gz -r20,Y | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -xs NA00003 /tmp/g8Is9I9_Su/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -xs NA00003 /tmp/g8Is9I9_Su/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/g8Is9I9_Su/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/g8Is9I9_Su/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -p /tmp/g8Is9I9_Su/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -p /tmp/g8Is9I9_Su/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -P /tmp/g8Is9I9_Su/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -P /tmp/g8Is9I9_Su/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/g8Is9I9_Su/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/g8Is9I9_Su/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -Hu /tmp/g8Is9I9_Su/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -GVsnps /tmp/g8Is9I9_Su/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -GVsnps /tmp/g8Is9I9_Su/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/g8Is9I9_Su/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/g8Is9I9_Su/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -s ^NA00003 /tmp/g8Is9I9_Su/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -s ^NA00003 /tmp/g8Is9I9_Su/view.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version /tmp/g8Is9I9_Su/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -G /tmp/g8Is9I9_Su/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -G /tmp/g8Is9I9_Su/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -HG /tmp/g8Is9I9_Su/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -a /tmp/g8Is9I9_Su/many.alleles.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -a /tmp/g8Is9I9_Su/many.alleles.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -asA /tmp/g8Is9I9_Su/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -asA /tmp/g8Is9I9_Su/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -asB /tmp/g8Is9I9_Su/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -asB /tmp/g8Is9I9_Su/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -asA /tmp/g8Is9I9_Su/view.vectors.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -asA /tmp/g8Is9I9_Su/view.vectors.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i'TXT0="text"' /tmp/g8Is9I9_Su/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1/test/view.chrs.tab /tmp/g8Is9I9_Su/view.chrs.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1/test/view.chrs.tab /tmp/g8Is9I9_Su/view.chrs.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -i 'POS>=3062917' /tmp/g8Is9I9_Su/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -i 'POS>=3062917' /tmp/g8Is9I9_Su/filter.2.vcf.gz 1:3062917-3157410 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/g8Is9I9_Su/idx.1.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/g8Is9I9_Su/idx.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1/test/idx.2.bed /tmp/g8Is9I9_Su/idx.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1/test/idx.3.bed /tmp/g8Is9I9_Su/idx.3.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.15.1/test/idx.4.bed /tmp/g8Is9I9_Su/idx.4.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -Ht 2 /tmp/g8Is9I9_Su/view-t.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -Ht 3 /tmp/g8Is9I9_Su/view-t.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/g8Is9I9_Su/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/g8Is9I9_Su/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/g8Is9I9_Su/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/g8Is9I9_Su/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/g8Is9I9_Su/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/g8Is9I9_Su/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/g8Is9I9_Su/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/g8Is9I9_Su/overlap.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/g8Is9I9_Su/overlap.vcf.gz .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.1.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.2.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.4.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.4.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_64bit: /builddir/build/BUILD/bcftools-1.15.1/bcftools view /builddir/build/BUILD/bcftools-1.15.1/test/view64bit.5.vcf -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -C5:nonmajor /tmp/g8Is9I9_Su/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -c6:nonmajor /tmp/g8Is9I9_Su/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -q0.3:major /tmp/g8Is9I9_Su/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/g8Is9I9_Su/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/g8Is9I9_Su/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/g8Is9I9_Su/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -H -a /tmp/g8Is9I9_Su/view-a.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1/test/view.sites.txt /tmp/g8Is9I9_Su/view.sites.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1/test/view.sites.txt /tmp/g8Is9I9_Su/view.sites.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.15.1/test/view.sites.txt.gz /tmp/g8Is9I9_Su/view.sites.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.15.1/test/view.sites.txt.gz /tmp/g8Is9I9_Su/view.sites.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -h 0 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -h 1 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -h 5 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -h 22 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -h 23 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -n 0 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -n 1 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -n 5 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_head: /builddir/build/BUILD/bcftools-1.15.1/bcftools head -h 5 -n 5 < /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mg0 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mg0 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -G /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -G /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.4.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.cals.1.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.cals.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mA -C alleles -T /tmp/g8Is9I9_Su/mpileup.cals.2.tab.gz /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.cals.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -cv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -cv /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ped /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.X.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.15.1/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.15.1/test/call-G.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.15.1/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/call-G.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.15.1/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.15.1/test/call-G.2.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.15.1/test/call-G.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -m /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -m /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.vcf .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.15.1/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.15.1/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.15.1/test/view.filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.15.1/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'ALT="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'ALT="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.15.1/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.15.1/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.15.1/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.15.1/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="A"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="A"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="RR"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="RR"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="RA"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="RA"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="AR"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="AR"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="AA"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="AA"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="aA"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="aA"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="HET"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="HET"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.15.1/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%POS\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.15.1/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.15.1/test/filter.7.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.15.1/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.15.1/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.15.1/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.15.1/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.15.1/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.15.1/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.15.1/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /builddir/build/BUILD/bcftools-1.15.1/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.15.1/bcftools sort -m 0 /builddir/build/BUILD/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.15.1/bcftools sort -Ob -m 0 /builddir/build/BUILD/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.15.1/bcftools sort -m 1000 /builddir/build/BUILD/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.15.1/bcftools sort -Ob -m 1000 /builddir/build/BUILD/bcftools-1.15.1/test/sort.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.15.1/test/regions.tab /tmp/g8Is9I9_Su/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.15.1/test/regions.tab .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /builddir/build/BUILD/bcftools-1.15.1/test/regions.tab /tmp/g8Is9I9_Su/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/g8Is9I9_Su/regions.tab.gz /tmp/g8Is9I9_Su/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/g8Is9I9_Su/regions.tab.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/g8Is9I9_Su/regions.tab.gz /tmp/g8Is9I9_Su/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/g8Is9I9_Su/regions.bed /tmp/g8Is9I9_Su/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/g8Is9I9_Su/regions.bed .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/g8Is9I9_Su/regions.bed /tmp/g8Is9I9_Su/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/g8Is9I9_Su/regions.bed.gz /tmp/g8Is9I9_Su/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/g8Is9I9_Su/regions.bed.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/g8Is9I9_Su/regions.bed.gz /tmp/g8Is9I9_Su/regions.vcf.gz .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/g8Is9I9_Su/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/g8Is9I9_Su/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -x FORMAT /builddir/build/BUILD/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -x FORMAT /builddir/build/BUILD/bcftools-1.15.1/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots4.vcf.gz -c +INFO /tmp/g8Is9I9_Su/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots4.vcf.gz -c +INFO /tmp/g8Is9I9_Su/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.15.1/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.15.1/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.15.1/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.15.1/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.15.1/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.15.1/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots11.vcf.gz -c FMT /tmp/g8Is9I9_Su/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots11.vcf.gz -c FMT /tmp/g8Is9I9_Su/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c FMT/newGT:=GT /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots2.vcf.gz -c FMT/newGT:=GT /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots12.vcf.gz -c FMT/GT:=newGT /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots12.vcf.gz -c FMT/GT:=newGT /tmp/g8Is9I9_Su/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.15.1/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.15.1/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.15.1/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /builddir/build/BUILD/bcftools-1.15.1/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -x FILTER /builddir/build/BUILD/bcftools-1.15.1/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -x FILTER /builddir/build/BUILD/bcftools-1.15.1/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/g8Is9I9_Su/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/g8Is9I9_Su/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/g8Is9I9_Su/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/g8Is9I9_Su/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate20.src.vcf.gz -c FMT/GT /tmp/g8Is9I9_Su/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate20.src.vcf.gz -c FMT/GT /tmp/g8Is9I9_Su/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate20.src.vcf.gz -c +FMT/GT /tmp/g8Is9I9_Su/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate20.src.vcf.gz -c +FMT/GT /tmp/g8Is9I9_Su/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate20.src.vcf.gz -c -FMT/GT /tmp/g8Is9I9_Su/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate20.src.vcf.gz -c -FMT/GT /tmp/g8Is9I9_Su/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.15.1/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.15.1/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.15.1/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate --rename-annots /builddir/build/BUILD/bcftools-1.15.1/test/annotate21.txt /builddir/build/BUILD/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob --rename-annots /builddir/build/BUILD/bcftools-1.15.1/test/annotate21.txt /builddir/build/BUILD/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /builddir/build/BUILD/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /builddir/build/BUILD/bcftools-1.15.1/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/g8Is9I9_Su/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/g8Is9I9_Su/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.15.1/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.15.1/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate24.src.vcf.gz -c XX /tmp/g8Is9I9_Su/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate24.src.vcf.gz -c XX /tmp/g8Is9I9_Su/annotate24.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.15.1/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /builddir/build/BUILD/bcftools-1.15.1/test/annotate25.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate26.tab.gz -c CHROM,POS,~POS /builddir/build/BUILD/bcftools-1.15.1/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate26.tab.gz -c CHROM,POS,~POS /builddir/build/BUILD/bcftools-1.15.1/test/annotate26.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /builddir/build/BUILD/bcftools-1.15.1/test/annotate.missing.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /builddir/build/BUILD/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 /builddir/build/BUILD/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 /builddir/build/BUILD/bcftools-1.15.1/test/annotate.olap.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots.id.vcf.gz -c ALT /tmp/g8Is9I9_Su/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots.id.vcf.gz -c ALT /tmp/g8Is9I9_Su/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -a /tmp/g8Is9I9_Su/annots.id.vcf.gz -c +ALT /tmp/g8Is9I9_Su/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate -Ob -a /tmp/g8Is9I9_Su/annots.id.vcf.gz -c +ALT /tmp/g8Is9I9_Su/annotate.id.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/g8Is9I9_Su/checkploidy.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/g8Is9I9_Su/checkploidy.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/g8Is9I9_Su/checkploidy.2.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/g8Is9I9_Su/checkploidy.2.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/g8Is9I9_Su/checkploidy.2.vcf.gz -- -m | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +check-ploidy --no-version /tmp/g8Is9I9_Su/checkploidy.2.bcf -- -m | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +missing2ref --no-version /tmp/g8Is9I9_Su/plugin1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +missing2ref --no-version /tmp/g8Is9I9_Su/plugin1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/plugin1.vcf.gz -- -t . -n 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/plugin1.bcf -- -t . -n 0 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.15.1/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.15.1/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.15.1/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.3.vcf.gz -- -t a -n pM | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.3.bcf -- -t a -n pM | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.3.vcf.gz -- -t a -n pm | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.3.bcf -- -t a -n pm | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.3.vcf.gz -- -t a -n c:1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.3.bcf -- -t a -n c:1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.3.vcf.gz -- -t a -n c:"1|1" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.3.bcf -- -t a -n c:"1|1" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.3.vcf.gz -- -t a -n c:"m|M" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.3.bcf -- -t a -n c:"m|M" | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.3.vcf.gz -- -t a -n c:0/1/1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.3.bcf -- -t a -n c:0/1/1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.4.bcf -- -t q -n . -e 'FMT/DP>90' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.4.vcf.gz -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +setGT --no-version /tmp/g8Is9I9_Su/setGT.4.bcf -- -t q -n . -e 'FMT/DP>100' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-AN-AC --no-version /tmp/g8Is9I9_Su/plugin1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-AN-AC --no-version /tmp/g8Is9I9_Su/plugin1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +dosage /tmp/g8Is9I9_Su/dosage.vcf.gz -- -t PL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +dosage /tmp/g8Is9I9_Su/dosage.bcf -- -t PL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +dosage /tmp/g8Is9I9_Su/dosage.vcf.gz -- -t GL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +dosage /tmp/g8Is9I9_Su/dosage.bcf -- -t GL | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +dosage /tmp/g8Is9I9_Su/dosage.vcf.gz -- -t GT | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +dosage /tmp/g8Is9I9_Su/dosage.bcf -- -t GT | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixploidy --no-version /tmp/g8Is9I9_Su/fixploidy.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.15.1/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.15.1/test/fixploidy.ploidy | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixploidy --no-version /tmp/g8Is9I9_Su/fixploidy.bcf -- -s /builddir/build/BUILD/bcftools-1.15.1/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.15.1/test/fixploidy.ploidy | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +guess-ploidy /tmp/g8Is9I9_Su/view.PL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +guess-ploidy /tmp/g8Is9I9_Su/view.PL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +guess-ploidy /tmp/g8Is9I9_Su/view.GL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +guess-ploidy /tmp/g8Is9I9_Su/view.GL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/g8Is9I9_Su/view.GL.vcf.gz -- -r --gl-to-pl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/g8Is9I9_Su/view.GL.bcf -- -r --gl-to-pl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/g8Is9I9_Su/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +tag2tag --no-version /tmp/g8Is9I9_Su/view.GP.bcf -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +add-variantkey /tmp/g8Is9I9_Su/query.variantkey.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +add-variantkey /tmp/g8Is9I9_Su/query.variantkey.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +variantkey-hex /tmp/g8Is9I9_Su/query.variantkey.vcf.gz test/ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +variantkey-hex /tmp/g8Is9I9_Su/query.variantkey.bcf test/ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +allele-length /tmp/g8Is9I9_Su/query.nucleotide.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +allele-length /tmp/g8Is9I9_Su/query.nucleotide.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/view.vcf.gz -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/view.bcf -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/view.vcf.gz -- -t AC -S /builddir/build/BUILD/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/view.bcf -- -t AC -S /builddir/build/BUILD/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/view.vcf.gz -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/view.bcf -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.15.1/test/fill-tags.3.smpl | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/many-alts.vcf.gz -- -t AN,AC | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/many-alts.bcf -- -t AN,AC | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-hemi.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-hemi.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-hemi.vcf.gz -- -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-hemi.bcf -- -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-hwe.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-hwe.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-hwe.vcf.gz -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-hwe.bcf -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-AN0.vcf.gz -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-AN0.bcf -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-VAF.vcf.gz -- -t VAF,VAF1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-VAF.bcf -- -t VAF,VAF1 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-AD.vcf.gz -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-AD.bcf -- -t 'INFO/DP:1=int(sum(INFO/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-AD.vcf.gz -- -t 'FORMAT/DP:1=int(smpl_sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-AD.bcf -- -t 'FORMAT/DP:1=int(smpl_sum(FMT/AD))' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-AD.vcf.gz -- -t 'XX=N_PASS(FMT/AD[:0]<=10)','YY=N_PASS(FMT/AD[:0]>10)' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-tags --no-version /tmp/g8Is9I9_Su/fill-tags-AD.bcf -- -t 'XX=N_PASS(FMT/AD[:0]<=10)','YY=N_PASS(FMT/AD[:0]>10)' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.vcf.gz | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.bcf | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.vcf.gz -- -H | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.bcf -- -H | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.vcf.gz -- -Hm | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.bcf -- -Hm | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.vcf.gz -- -Hmv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.bcf -- -Hmv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.vcf.gz -- -Hv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.bcf -- -Hv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.vcf.gz -- -m | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.bcf -- -m | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.vcf.gz -- -mv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.bcf -- -mv | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.vcf.gz -- -v | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTisec /tmp/g8Is9I9_Su/view.bcf -- -v | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-switch-rate /tmp/g8Is9I9_Su/trio.vcf.gz -- -p /builddir/build/BUILD/bcftools-1.15.1/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-switch-rate /tmp/g8Is9I9_Su/trio.bcf -- -p /builddir/build/BUILD/bcftools-1.15.1/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-stats /tmp/g8Is9I9_Su/trio-stats.vcf.gz -a 1 -p /builddir/build/BUILD/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-stats /tmp/g8Is9I9_Su/trio-stats.bcf -a 1 -p /builddir/build/BUILD/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-stats /tmp/g8Is9I9_Su/trio-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-stats /tmp/g8Is9I9_Su/trio-stats.bcf -p /builddir/build/BUILD/bcftools-1.15.1/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +smpl-stats /tmp/g8Is9I9_Su/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +smpl-stats /tmp/g8Is9I9_Su/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +indel-stats /tmp/g8Is9I9_Su/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +indel-stats /tmp/g8Is9I9_Su/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +indel-stats /tmp/g8Is9I9_Su/indel-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.15.1/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +indel-stats /tmp/g8Is9I9_Su/indel-stats.bcf -p /builddir/build/BUILD/bcftools-1.15.1/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +indel-stats /tmp/g8Is9I9_Su/indel-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.15.1/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +indel-stats /tmp/g8Is9I9_Su/indel-stats.bcf -p /builddir/build/BUILD/bcftools-1.15.1/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +ad-bias /tmp/g8Is9I9_Su/ad-bias.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +ad-bias /tmp/g8Is9I9_Su/ad-bias.bcf -- -s /builddir/build/BUILD/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +ad-bias /tmp/g8Is9I9_Su/ad-bias.2.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +ad-bias /tmp/g8Is9I9_Su/ad-bias.2.bcf -- -s /builddir/build/BUILD/bcftools-1.15.1/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +ad-bias /tmp/g8Is9I9_Su/ad-bias.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +ad-bias /tmp/g8Is9I9_Su/ad-bias.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +ad-bias /tmp/g8Is9I9_Su/ad-bias.2.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +ad-bias /tmp/g8Is9I9_Su/ad-bias.2.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.15.1/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +af-dist /tmp/g8Is9I9_Su/af-dist.vcf.gz | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +af-dist /tmp/g8Is9I9_Su/af-dist.bcf | grep -v bcftools | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/g8Is9I9_Su/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -i /tmp/g8Is9I9_Su/fixref.2b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/g8Is9I9_Su/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -i /tmp/g8Is9I9_Su/fixref.2b.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/g8Is9I9_Su/fixref.3.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1/test/fixref.3.fa -m top | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/g8Is9I9_Su/fixref.3.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1/test/fixref.3.fa -m top | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/g8Is9I9_Su/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -m ref-alt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/g8Is9I9_Su/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -m ref-alt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/g8Is9I9_Su/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -m flip | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/g8Is9I9_Su/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -m flip | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/g8Is9I9_Su/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -m flip-all | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fixref /tmp/g8Is9I9_Su/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -m flip-all | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/g8Is9I9_Su/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.15.1/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/g8Is9I9_Su/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.15.1/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/g8Is9I9_Su/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1/test/aa.fa -c REF -N | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/g8Is9I9_Su/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1/test/aa.fa -c REF -N | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/g8Is9I9_Su/ref.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -c REF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +fill-from-fasta /tmp/g8Is9I9_Su/ref.bcf -- -f /builddir/build/BUILD/bcftools-1.15.1/test/norm.fa -c REF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/g8Is9I9_Su/view.vcf.gz -- -s NA00001 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/g8Is9I9_Su/view.bcf -- -s NA00001 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/g8Is9I9_Su/view.vcf.gz -- -s NA00001,NA00002 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/g8Is9I9_Su/view.bcf -- -s NA00001,NA00002 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/g8Is9I9_Su/view.vcf.gz -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +GTsubset --no-version /tmp/g8Is9I9_Su/view.bcf -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/g8Is9I9_Su/mendelian.vcf.gz -t mom1,dad1,child1 -md | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/g8Is9I9_Su/mendelian.bcf -t mom1,dad1,child1 -md | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/g8Is9I9_Su/mendelian.vcf.gz -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/g8Is9I9_Su/mendelian.bcf -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/g8Is9I9_Su/mendelian.vcf.gz -t mom1,dad1,child1 -mx | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/g8Is9I9_Su/mendelian.bcf -t mom1,dad1,child1 -mx | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/g8Is9I9_Su/mendelian.vcf.gz -t mom1,dad1,child1 -ma | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/g8Is9I9_Su/mendelian.bcf -t mom1,dad1,child1 -ma | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/g8Is9I9_Su/mendelian.vcf.gz -t mom1,dad1,child1 -mu | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +mendelian /tmp/g8Is9I9_Su/mendelian.bcf -t mom1,dad1,child1 -mu | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/g8Is9I9_Su/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/g8Is9I9_Su/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/g8Is9I9_Su/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.15.1/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.15.1/test/contrast1.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/g8Is9I9_Su/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.15.1/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.15.1/test/contrast1.txt | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/g8Is9I9_Su/contrast.vcf.gz -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/g8Is9I9_Su/contrast.bcf -a NASSOC -0 a,b,c -1 d --force-samples | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/g8Is9I9_Su/contrast.1.vcf.gz -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/g8Is9I9_Su/contrast.1.bcf -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/g8Is9I9_Su/contrast.1.vcf.gz -a NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +contrast /tmp/g8Is9I9_Su/contrast.1.bcf -a NOVELGT -0 A -1 B | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.1.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.1.bcf -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.2.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.2.bcf -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.4.bcf -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.8.vcf.gz -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.8.bcf -p proband,father,mother | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.9.vcf.gz -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.9.bcf -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.9.vcf.gz -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.9.bcf -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.10.vcf.gz -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +trio-dnm2 /tmp/g8Is9I9_Su/trio-dnm/trio-dnm.10.bcf -p proband,father,mother --with-pAD | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[\t%DNM][\t%VAF]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +gvcfz /tmp/g8Is9I9_Su/gvcfz.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +gvcfz /tmp/g8Is9I9_Su/gvcfz.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +gvcfz /tmp/g8Is9I9_Su/gvcfz.vcf.gz -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +gvcfz /tmp/g8Is9I9_Su/gvcfz.bcf -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +gvcfz /tmp/g8Is9I9_Su/gvcfz.2.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +gvcfz /tmp/g8Is9I9_Su/gvcfz.2.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +remove-overlaps /tmp/g8Is9I9_Su/remove-overlaps.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +remove-overlaps /tmp/g8Is9I9_Su/remove-overlaps.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +remove-overlaps /tmp/g8Is9I9_Su/remove-overlaps.vcf.gz -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +remove-overlaps /tmp/g8Is9I9_Su/remove-overlaps.bcf -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.vcf.gz -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.bcf -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.vcf.gz -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.bcf -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.vcf.gz -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.bcf -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.2.vcf.gz -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.2.bcf -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.2.vcf.gz -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.2.bcf -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.3.vcf.gz -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.3.bcf -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.3.vcf.gz -s worst -f'[%POS\t%SAMPLE\t%GT\t%Consequence\n]' -i'GT="alt"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.3.bcf -s worst -f'[%POS\t%SAMPLE\t%GT\t%Consequence\n]' -i'GT="alt"' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.4.bcf -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.vcf.gz -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.bcf -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.vcf.gz -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.bcf -c gnomAD_NFE_AF,ALLELE_NUM | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.5.vcf.gz -s :synonymous -c Consequence | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.5.bcf -s :synonymous -c Consequence | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.5.vcf.gz -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.5.bcf -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.6.vcf.gz -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.6.bcf -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.6.vcf.gz -c - | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.6.bcf -c - | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.6.vcf.gz -c - -s worst | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.6.bcf -c - -s worst | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.7.vcf.gz --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.7.bcf --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.8.vcf.gz -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.8.bcf -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.8.vcf.gz -a BCSQ -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.8.bcf -a BCSQ -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.9.vcf.gz -a BCSQ -f '%CHROM\t%POS\t%REF\t%ALT\t%BCSQ\n' -d -A tab | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.9.bcf -a BCSQ -f '%CHROM\t%POS\t%REF\t%ALT\t%BCSQ\n' -d -A tab | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.9.vcf.gz -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.9.bcf -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.10.vcf.gz -a CSQ -f '%M_CAP_pred %M_CAP_score\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.10.bcf -a CSQ -f '%M_CAP_pred %M_CAP_score\n' | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.10.vcf.gz -a CSQ -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split-vep /tmp/g8Is9I9_Su/split-vep.10.bcf -a CSQ -f '%xM_CAP_pred %xM_CAP_score\n' -p x | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +parental-origin /tmp/g8Is9I9_Su/parental-origin.vcf.gz -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +parental-origin /tmp/g8Is9I9_Su/parental-origin.bcf -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +parental-origin /tmp/g8Is9I9_Su/parental-origin.vcf.gz -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +parental-origin /tmp/g8Is9I9_Su/parental-origin.bcf -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +parental-origin /tmp/g8Is9I9_Su/parental-origin.vcf.gz -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +parental-origin /tmp/g8Is9I9_Su/parental-origin.bcf -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +parental-origin /tmp/g8Is9I9_Su/parental-origin.vcf.gz -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +parental-origin /tmp/g8Is9I9_Su/parental-origin.bcf -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +parental-origin /tmp/g8Is9I9_Su/parental-origin.vcf.gz -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +parental-origin /tmp/g8Is9I9_Su/parental-origin.bcf -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/g8Is9I9_Su/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/g8Is9I9_Su/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/g8Is9I9_Su/prune.2.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 1 -a r2,LD,HD /tmp/g8Is9I9_Su/prune.2.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/g8Is9I9_Su/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/g8Is9I9_Su/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/g8Is9I9_Su/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2 -a r2 -m 0.5 /tmp/g8Is9I9_Su/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/g8Is9I9_Su/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/g8Is9I9_Su/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/g8Is9I9_Su/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/g8Is9I9_Su/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N 1st /tmp/g8Is9I9_Su/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N 1st /tmp/g8Is9I9_Su/prune.1.bcf | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/g8Is9I9_Su/prune.1.vcf.gz | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.15.1/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/g8Is9I9_Su/prune.1.bcf | grep -v ^##bcftools_ .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/g8Is9I9_Su/split.1.1 && cd /tmp/g8Is9I9_Su/split.1.1 && for f in A1.vcf A2.vcf A3.vcf B1.vcf B2.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/g8Is9I9_Su/split.1.2 -S /builddir/build/BUILD/bcftools-1.15.1/test/split.smpl.1.2.txt && cd /tmp/g8Is9I9_Su/split.1.2 && for f in A.vcf B.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/g8Is9I9_Su/split.1.3 -S /builddir/build/BUILD/bcftools-1.15.1/test/split.smpl.1.3.txt && cd /tmp/g8Is9I9_Su/split.1.3 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/g8Is9I9_Su/split.1.4 -S /builddir/build/BUILD/bcftools-1.15.1/test/split.smpl.1.3.txt -i 'GT[0]="alt"' && cd /tmp/g8Is9I9_Su/split.1.4 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/g8Is9I9_Su/split.1.5 -S /builddir/build/BUILD/bcftools-1.15.1/test/split.smpl.1.3.txt -i 'GT="alt"' && cd /tmp/g8Is9I9_Su/split.1.5 && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/g8Is9I9_Su/split.1.6 -S /builddir/build/BUILD/bcftools-1.15.1/test/split.smpl.1.4.txt -i 'GT="alt"' && cd /tmp/g8Is9I9_Su/split.1.6 && for f in file1.vcf file2.vcf file3.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.1.vcf -o /tmp/g8Is9I9_Su/split.1.7 -G /builddir/build/BUILD/bcftools-1.15.1/test/split.grp.1.1.txt && cd /tmp/g8Is9I9_Su/split.1.7 && for f in A.vcf A1.vcf A2.vcf B.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_split: /builddir/build/BUILD/bcftools-1.15.1/bcftools +split /builddir/build/BUILD/bcftools-1.15.1/test/split.2.vcf -o /tmp/g8Is9I9_Su/split.2.1 && cd /tmp/g8Is9I9_Su/split.2.1 && for f in A1_A1-1.vcf A1_A1-2.vcf A1_A1.vcf B1.vcf B2.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H $f; done .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/g8Is9I9_Su/scatter.1.1 -n 3 && cd /tmp/g8Is9I9_Su/scatter.1.1 && cat 0.vcf 1.vcf 2.vcf | grep -v ^## .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/g8Is9I9_Su/scatter.1.2 -s 21,22 && cd /tmp/g8Is9I9_Su/scatter.1.2 && cat 21.vcf 22.vcf | grep -v ^## .. ok test_plugin_scatter: /builddir/build/BUILD/bcftools-1.15.1/bcftools +scatter /builddir/build/BUILD/bcftools-1.15.1/test/scatter.1.vcf -o /tmp/g8Is9I9_Su/scatter.1.3 -s 21,22 -x X && cd /tmp/g8Is9I9_Su/scatter.1.3 && cat 21.vcf 22.vcf X.vcf | grep -v ^## .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version /tmp/g8Is9I9_Su/concat.1.a.vcf.gz /tmp/g8Is9I9_Su/concat.1.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob /tmp/g8Is9I9_Su/concat.1.a.vcf.gz /tmp/g8Is9I9_Su/concat.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version /tmp/g8Is9I9_Su/concat.1.a.bcf /tmp/g8Is9I9_Su/concat.1.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob /tmp/g8Is9I9_Su/concat.1.a.bcf /tmp/g8Is9I9_Su/concat.1.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -a /tmp/g8Is9I9_Su/concat.2.a.vcf.gz /tmp/g8Is9I9_Su/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -a /tmp/g8Is9I9_Su/concat.2.a.vcf.gz /tmp/g8Is9I9_Su/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -a /tmp/g8Is9I9_Su/concat.2.a.bcf /tmp/g8Is9I9_Su/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -a /tmp/g8Is9I9_Su/concat.2.a.bcf /tmp/g8Is9I9_Su/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -aD /tmp/g8Is9I9_Su/concat.2.a.vcf.gz /tmp/g8Is9I9_Su/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -aD /tmp/g8Is9I9_Su/concat.2.a.vcf.gz /tmp/g8Is9I9_Su/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -aD /tmp/g8Is9I9_Su/concat.2.a.bcf /tmp/g8Is9I9_Su/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -aD /tmp/g8Is9I9_Su/concat.2.a.bcf /tmp/g8Is9I9_Su/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/g8Is9I9_Su/concat.3.a.vcf.gz /tmp/g8Is9I9_Su/concat.3.b.vcf.gz /tmp/g8Is9I9_Su/concat.3.0.vcf.gz /tmp/g8Is9I9_Su/concat.3.c.vcf.gz /tmp/g8Is9I9_Su/concat.3.d.vcf.gz /tmp/g8Is9I9_Su/concat.3.e.vcf.gz /tmp/g8Is9I9_Su/concat.3.f.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/g8Is9I9_Su/concat.3.a.vcf.gz /tmp/g8Is9I9_Su/concat.3.b.vcf.gz /tmp/g8Is9I9_Su/concat.3.0.vcf.gz /tmp/g8Is9I9_Su/concat.3.c.vcf.gz /tmp/g8Is9I9_Su/concat.3.d.vcf.gz /tmp/g8Is9I9_Su/concat.3.e.vcf.gz /tmp/g8Is9I9_Su/concat.3.f.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/g8Is9I9_Su/concat.3.a.bcf /tmp/g8Is9I9_Su/concat.3.b.bcf /tmp/g8Is9I9_Su/concat.3.0.bcf /tmp/g8Is9I9_Su/concat.3.c.bcf /tmp/g8Is9I9_Su/concat.3.d.bcf /tmp/g8Is9I9_Su/concat.3.e.bcf /tmp/g8Is9I9_Su/concat.3.f.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/g8Is9I9_Su/concat.3.a.bcf /tmp/g8Is9I9_Su/concat.3.b.bcf /tmp/g8Is9I9_Su/concat.3.0.bcf /tmp/g8Is9I9_Su/concat.3.c.bcf /tmp/g8Is9I9_Su/concat.3.d.bcf /tmp/g8Is9I9_Su/concat.3.e.bcf /tmp/g8Is9I9_Su/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 2034645000 .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --naive-force /tmp/g8Is9I9_Su/naive_concat.0.bcf /tmp/g8Is9I9_Su/naive_concat.1.bcf /tmp/g8Is9I9_Su/naive_concat.2.bcf /tmp/g8Is9I9_Su/naive_concat.3.bcf /tmp/g8Is9I9_Su/naive_concat.4.bcf /tmp/g8Is9I9_Su/naive_concat.5.bcf /tmp/g8Is9I9_Su/naive_concat.6.bcf /tmp/g8Is9I9_Su/naive_concat.7.bcf /tmp/g8Is9I9_Su/naive_concat.8.bcf /tmp/g8Is9I9_Su/naive_concat.9.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --naive /tmp/g8Is9I9_Su/naive_concat.0.vcf.gz /tmp/g8Is9I9_Su/naive_concat.1.vcf.gz /tmp/g8Is9I9_Su/naive_concat.2.vcf.gz /tmp/g8Is9I9_Su/naive_concat.3.vcf.gz /tmp/g8Is9I9_Su/naive_concat.4.vcf.gz /tmp/g8Is9I9_Su/naive_concat.5.vcf.gz /tmp/g8Is9I9_Su/naive_concat.6.vcf.gz /tmp/g8Is9I9_Su/naive_concat.7.vcf.gz /tmp/g8Is9I9_Su/naive_concat.8.vcf.gz /tmp/g8Is9I9_Su/naive_concat.9.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view -H .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l /tmp/g8Is9I9_Su/concat.4.a.vcf.gz /tmp/g8Is9I9_Su/concat.4.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l /tmp/g8Is9I9_Su/concat.4.a.vcf.gz /tmp/g8Is9I9_Su/concat.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l /tmp/g8Is9I9_Su/concat.4.a.bcf /tmp/g8Is9I9_Su/concat.4.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l /tmp/g8Is9I9_Su/concat.4.a.bcf /tmp/g8Is9I9_Su/concat.4.b.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/g8Is9I9_Su/concat.5.a.vcf.gz /tmp/g8Is9I9_Su/concat.5.b.vcf.gz /tmp/g8Is9I9_Su/concat.5.c.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/g8Is9I9_Su/concat.5.a.vcf.gz /tmp/g8Is9I9_Su/concat.5.b.vcf.gz /tmp/g8Is9I9_Su/concat.5.c.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l --ligate-warn /tmp/g8Is9I9_Su/concat.5.a.bcf /tmp/g8Is9I9_Su/concat.5.b.bcf /tmp/g8Is9I9_Su/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l --ligate-warn /tmp/g8Is9I9_Su/concat.5.a.bcf /tmp/g8Is9I9_Su/concat.5.b.bcf /tmp/g8Is9I9_Su/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat --no-version -l --ligate-force /tmp/g8Is9I9_Su/concat.5.a.bcf /tmp/g8Is9I9_Su/concat.5.b.bcf /tmp/g8Is9I9_Su/concat.5.c.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.15.1/bcftools concat -Ob -l --ligate-force /tmp/g8Is9I9_Su/concat.5.a.bcf /tmp/g8Is9I9_Su/concat.5.b.bcf /tmp/g8Is9I9_Su/concat.5.c.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.hdr /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.hdr /tmp/g8Is9I9_Su/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/g8Is9I9_Su/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.hdr /tmp/g8Is9I9_Su/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/g8Is9I9_Su/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples /tmp/g8Is9I9_Su/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/g8Is9I9_Su/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples /tmp/g8Is9I9_Su/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/g8Is9I9_Su/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples2 /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples2 /tmp/g8Is9I9_Su/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/g8Is9I9_Su/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples2 /tmp/g8Is9I9_Su/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/g8Is9I9_Su/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples3 /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples3 /tmp/g8Is9I9_Su/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/g8Is9I9_Su/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples3 /tmp/g8Is9I9_Su/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/g8Is9I9_Su/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples4 /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples4 /tmp/g8Is9I9_Su/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/g8Is9I9_Su/reheader.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples4 /tmp/g8Is9I9_Su/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/g8Is9I9_Su/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -s /builddir/build/BUILD/bcftools-1.15.1/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.empty.hdr /builddir/build/BUILD/bcftools-1.15.1/test/empty.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.15.1/test/empty.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.empty.hdr /tmp/g8Is9I9_Su/empty.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/g8Is9I9_Su/empty.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.empty.hdr /tmp/g8Is9I9_Su/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/g8Is9I9_Su/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1/test/reheader.fai /builddir/build/BUILD/bcftools-1.15.1/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1/test/reheader.fai /tmp/g8Is9I9_Su/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -f /builddir/build/BUILD/bcftools-1.15.1/test/reheader.fai /tmp/g8Is9I9_Su/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1/test/reheader.fai /builddir/build/BUILD/bcftools-1.15.1/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1/test/reheader.fai /tmp/g8Is9I9_Su/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.15.1/bcftools reheader -h /builddir/build/BUILD/bcftools-1.15.1/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.15.1/test/reheader.fai /tmp/g8Is9I9_Su/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools view --no-version .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/g8Is9I9_Su/rename.map -Ov /tmp/g8Is9I9_Su/annotate.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/g8Is9I9_Su/rename.map -Ob /tmp/g8Is9I9_Su/annotate.bcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/g8Is9I9_Su/rename.map -Ov /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.15.1/bcftools annotate --rename-chrs /tmp/g8Is9I9_Su/rename.map -Ob /builddir/build/BUILD/bcftools-1.15.1/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. /tmp/g8Is9I9_Su/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids /tmp/g8Is9I9_Su/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids --3N6 /tmp/g8Is9I9_Su/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- /tmp/g8Is9I9_Su/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --vcf-ids -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -G /builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.ids.gen.rev,/builddir/build/BUILD/bcftools-1.15.1/test/convert.gs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --tag PL /tmp/g8Is9I9_Su/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --tag PL /tmp/g8Is9I9_Su/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids /tmp/g8Is9I9_Su/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --vcf-ids /tmp/g8Is9I9_Su/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --3N6 /tmp/g8Is9I9_Su/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --3N6 /tmp/g8Is9I9_Su/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --3N6 --vcf-ids /tmp/g8Is9I9_Su/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --3N6 --vcf-ids /tmp/g8Is9I9_Su/check.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/check.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h -,.,. /tmp/g8Is9I9_Su/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h -,.,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h .,-,. /tmp/g8Is9I9_Su/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h .,-,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h .,-,. --vcf-ids /tmp/g8Is9I9_Su/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h .,.,- /tmp/g8Is9I9_Su/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -H /builddir/build/BUILD/bcftools-1.15.1/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -H /builddir/build/BUILD/bcftools-1.15.1/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hls.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --haplegendsample -,.,. /tmp/g8Is9I9_Su/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.hap-missing.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample -,. /tmp/g8Is9I9_Su/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample -,. .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample -,. --vcf-ids /tmp/g8Is9I9_Su/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample .,- /tmp/g8Is9I9_Su/convert.vcf.gz .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.ids.hap,/builddir/build/BUILD/bcftools-1.15.1/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa /tmp/g8Is9I9_Su/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools view -Ob /tmp/g8Is9I9_Su/convert.gvcf.vcf.gz | /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.15.1/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.15.1/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.15.1/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.15.1/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.15.1/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.15.1/test/convert.23andme | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab -c /tmp/g8Is9I9_Su/consensus.1.chain.new >/dev/null; cat /tmp/g8Is9I9_Su/consensus.1.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab -c /tmp/g8Is9I9_Su/consensus.2.chain.new >/dev/null; cat /tmp/g8Is9I9_Su/consensus.2.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab --mask-with X -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.tab -c /tmp/g8Is9I9_Su/consensus.3.chain.new >/dev/null; cat /tmp/g8Is9I9_Su/consensus.3.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -H 1 -c /tmp/g8Is9I9_Su/consensus.4.chain.new >/dev/null; cat /tmp/g8Is9I9_Su/consensus.4.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/empty.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus4.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus2.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus5.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus6.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus6.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -a . .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -a . -i 'ALT!=""' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -a . -e 'MinDP>15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -a . -e 'MinDP<15' .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.12.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.13.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.13.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.14.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.14.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.12.fa --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.15.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -I .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.fa -H I .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.17.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus2.fa -M N -m /builddir/build/BUILD/bcftools-1.15.1/test/consensus.17.bed .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.18.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.18.fa .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.15.1/bcftools consensus /tmp/g8Is9I9_Su/consensus.19.vcf.gz -f /builddir/build/BUILD/bcftools-1.15.1/test/consensus.19.fa .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -b /tmp/g8Is9I9_Su/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob -b /tmp/g8Is9I9_Su/mpileup.bam.urllist | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -b /tmp/g8Is9I9_Su/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob -b /tmp/g8Is9I9_Su/mpileup.cram.urllist | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/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 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/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 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/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 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/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 /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.15.1/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.15.1/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.sam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.15.1/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.1.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.bam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.cram | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.15.1/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.15.1/test/mpileup/mpileup-filter.sam | /builddir/build/BUILD/bcftools-1.15.1/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq.gff3 /builddir/build/BUILD/bcftools-1.15.1/test/csq.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq.chr.gff3 /builddir/build/BUILD/bcftools-1.15.1/test/csq.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq.2.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq.2.gff --ncsq 64 /builddir/build/BUILD/bcftools-1.15.1/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000624631/ENST00000624631.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000624631/ENST00000624631.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000624631/ambiguous.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000593942/ENST00000593942.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000593942/ENST00000593942.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000593942/last-codon-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/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 /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000580206 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000557788/ENST00000557788.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000557788/ENST00000557788.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000557788/long-overlap-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000545279/ENST00000545279.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000545279/ENST00000545279.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000545279/splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000528237/ENST00000528237.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000528237/ENST00000528237.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520868/ENST00000520868.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520868/ENST00000520868.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520868/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000519442/ENST00000519442.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000519442/ENST00000519442.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000519442/synon-splice-region-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000518414/ENST00000518414.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000518414/ENST00000518414.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000448695/ENST00000448695.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000448695/ENST00000448695.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000436063/ENST00000436063.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000436063/ENST00000436063.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000436063/insert-before-utr.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/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 /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000422159 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420670/start-stop-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420670/segfault.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420190/ENST00000420190.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420190/ENST00000420190.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000420190/abort-in-csq-push.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000413103/ENST00000413103.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000413103/ENST00000413103.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000413103/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000410009/ENST00000410009.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000410009/ENST00000410009.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000410009/frameshift.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/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 /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000409523/ENST00000409523.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000409523/ENST00000409523.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000409523/long-overlapping-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000400151/ENST00000400151.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000400151/ENST00000400151.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000400151/long-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000390520/ENST00000390520.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000390520/ENST00000390520.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000390520/deletion-overlap.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000382647/ENST00000382647.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000382647/ENST00000382647.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000381157/ENST00000381157.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000381157/ENST00000381157.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000381157/haploid-diploid.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000379416 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000375992/ENST00000375992.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000375992/ENST00000375992.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000368801/ENST00000368801.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000368801/ENST00000368801.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000368801/compound-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000368801.2/ENST00000368801.2.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000368801.2/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000357367/ENST00000357367.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000357367/ENST00000357367.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000357367/stop-retained.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249.2/ENST00000318249.2.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000301246/ENST00000301246.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000301246/ENST00000301246.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000301246/15bp-insert.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000285021/ENST00000285021.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000285021/ENST00000285021.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000271583/ENST00000271583.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000271583/ENST00000271583.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000271583/splice-acceptor.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000269081/ENST00000269081.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000269081/ENST00000269081.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000263103-INS/insertions.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000256452/ENST00000256452.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000256452/ENST00000256452.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000256452/intron.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000230048/ENST00000230048.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000230048/ENST00000230048.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000230048/start-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000227471/ENST00000227471.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000227471/ENST00000227471.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000218032/start-lost-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/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 /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENST00000000000 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENSMUST00000133836 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENSG00000173376/ENSG00000173376.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENSG00000173376/ENSG00000173376.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/ENSG00000173376/synon.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/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 /builddir/build/BUILD/bcftools-1.15.1/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/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 /builddir/build/BUILD/bcftools-1.15.1/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0003/EDUMMY0003.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0003/EDUMMY0003.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0003/long-del.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0002/EDUMMY0002.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0002/EDUMMY0002.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0002/boundaries.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.15.1/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.15.1/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.15.1/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.15.1/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.15.1/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.15.1/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /builddir/build/BUILD/bcftools-1.15.1/bcftools roh /builddir/build/BUILD/bcftools-1.15.1/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/g8Is9I9_Su/gtcheck.1.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,GT /tmp/g8Is9I9_Su/gtcheck.1.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,PL /tmp/g8Is9I9_Su/gtcheck.1.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,GT /tmp/g8Is9I9_Su/gtcheck.1.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,PL /tmp/g8Is9I9_Su/gtcheck.1.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -p s1,s1 /tmp/g8Is9I9_Su/gtcheck.1.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/g8Is9I9_Su/gtcheck.2.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 /tmp/g8Is9I9_Su/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/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/g8Is9I9_Su/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1/test/gtcheck.3.pairs /tmp/g8Is9I9_Su/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL /tmp/g8Is9I9_Su/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 --n-matches 4 /tmp/g8Is9I9_Su/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/g8Is9I9_Su/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/g8Is9I9_Su/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/g8Is9I9_Su/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/g8Is9I9_Su/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/g8Is9I9_Su/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -p B,C,B,D /tmp/g8Is9I9_Su/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,GT -H /tmp/g8Is9I9_Su/gtcheck.1.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u GT,PL -H /tmp/g8Is9I9_Su/gtcheck.1.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,GT -H /tmp/g8Is9I9_Su/gtcheck.1.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -u PL,PL -H /tmp/g8Is9I9_Su/gtcheck.1.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/g8Is9I9_Su/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.15.1/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/g8Is9I9_Su/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -u GT -e 30 /tmp/g8Is9I9_Su/gtcheck.1.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/g8Is9I9_Su/gtcheck.1.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -u GT -e 300 /tmp/g8Is9I9_Su/gtcheck.1.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck -u PL -e 30 /tmp/g8Is9I9_Su/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck /tmp/g8Is9I9_Su/gtcheck.ntop.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck --n-matches 2 /tmp/g8Is9I9_Su/gtcheck.ntop.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /builddir/build/BUILD/bcftools-1.15.1/bcftools gtcheck /tmp/g8Is9I9_Su/gtcheck.5.vcf.gz -g /tmp/g8Is9I9_Su/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok Number of tests: total .. 1723 passed .. 1723 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: bcftools-1.15.1-2.fc38.i686 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.fFxIOY + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.15.1 + DOCDIR=/builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/share/doc/bcftools + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/share/doc/bcftools + cp -pr AUTHORS /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/share/doc/bcftools + cp -pr NEWS /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/share/doc/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.uoskAq + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.15.1 + LICENSEDIR=/builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/share/licenses/bcftools + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/share/licenses/bcftools + cp -pr LICENSE /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386/usr/share/licenses/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Provides: bcftools = 1.15.1-2.fc38 bcftools(x86-32) = 1.15.1-2.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl /usr/bin/python3 libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.33) libc.so.6(GLIBC_2.34) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libgsl.so.27 libgslcblas.so.0 libhts.so.3 libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libm.so.6(GLIBC_2.23) libm.so.6(GLIBC_2.29) libperl.so.5.36 libz.so.1 rtld(GNU_HASH) Conflicts: samtools < 1.0 Processing files: bcftools-debugsource-1.15.1-2.fc38.i686 Provides: bcftools-debugsource = 1.15.1-2.fc38 bcftools-debugsource(x86-32) = 1.15.1-2.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bcftools-debuginfo-1.15.1-2.fc38.i686 Provides: bcftools-debuginfo = 1.15.1-2.fc38 bcftools-debuginfo(x86-32) = 1.15.1-2.fc38 debuginfo(build-id) = 012167001524d56f9ee44487c2906d7a218926cf debuginfo(build-id) = 01dc7f764ae9f553cf07e2cd94f25e778d7f8516 debuginfo(build-id) = 157e01286fe3cc23aa43720135d62b8d5abeb3b4 debuginfo(build-id) = 199c5c78afb10d29c7371fdf080656c64e0a7ab9 debuginfo(build-id) = 19b24f1cdd0af84a624efecbfa88f7c1082a307c debuginfo(build-id) = 2069bf6cbba88f3d840e607f7ddafbb27a956014 debuginfo(build-id) = 2d15c3e7178f45305d961e4a65b3f976a5431b60 debuginfo(build-id) = 31ce54f1a4fce76e2d868d65c9061146a2384253 debuginfo(build-id) = 31e67eecae1b0e7457b07d25e499d1b211157054 debuginfo(build-id) = 376f15d0cffe25b101cd91074db7c75347f23e53 debuginfo(build-id) = 3974b4bdfa17f83509d3365893fe9fdd812ccf5f debuginfo(build-id) = 4c487e26762adec739cb72eaa41387e47739865e debuginfo(build-id) = 510c4e7fe76a6d047d5b5737d51ad0367dec863a debuginfo(build-id) = 57dc27c8192dbc4f51c6617c0150bcb5e5d454a4 debuginfo(build-id) = 58db94cf93acd02de7c702c7c563a088cd0910e0 debuginfo(build-id) = 5bafd05d92c4edd3e3d21d590d2d906f8b467c23 debuginfo(build-id) = 5cad4d008e3e9ec28f89f5e2d34381946a077508 debuginfo(build-id) = 609fe565c9546d9a8bdb5b3e64fddc36fd8c53ce debuginfo(build-id) = 625c84ff7e50ccff5a6a28b49d7fc575daa8f3be debuginfo(build-id) = 64eb39ceb7eb2746153a136be54fd23e86eb5454 debuginfo(build-id) = 68b67421ac6d0a3444a543226011d081c58e832d debuginfo(build-id) = 7e04eb1c8df867d91cf318b32fbb093e4d20a66b debuginfo(build-id) = 88965817df14c0f22f23caeb6fb0e024e080e1b1 debuginfo(build-id) = 9c723ca5c14705ced1a22c905534055b2be6a62a debuginfo(build-id) = a5fe2b4b35138f9c436e06a81dbf99488f4d4435 debuginfo(build-id) = b20b172d3c386f7dd96c34b7b0b969b0298b6dc3 debuginfo(build-id) = ba44309ce1fa74e77eb87c1047c4070a5dddea93 debuginfo(build-id) = c83d44869d3d8f6a5238e62fb3ffeba4a2fae564 debuginfo(build-id) = d33bc6ba8f6e3c2f1a5634004fc350c0534b7c62 debuginfo(build-id) = d3dee0dac42aa242ed80493f038c58e5a91860e3 debuginfo(build-id) = d3f474a59d4701f5a91c71076eaeb44871f49ec2 debuginfo(build-id) = d4595b40e374f1d04abac9c13f9b973b8a1677b8 debuginfo(build-id) = d57cf62da85ff657419a23d9a00beb773e42af59 debuginfo(build-id) = e49231403a9e4b9db2ad9684a91ab40554f548b0 debuginfo(build-id) = e6b542e73faeed758c6c804b314f866d6e1fa492 debuginfo(build-id) = eba2bdb90d963210f90170f572c799ef39d608b6 debuginfo(build-id) = f3b014bca64effcbfdf7ad26d1c84e3093bc854a debuginfo(build-id) = f93166c278493217f43736bb0e58b3b511e57c6e debuginfo(build-id) = fd6ee12a9d7ecae8d14c25c19d257e25aa1bc37c Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bcftools-debugsource(x86-32) = 1.15.1-2.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386 Wrote: /builddir/build/RPMS/bcftools-debugsource-1.15.1-2.fc38.i686.rpm Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.15.1-2.fc38.i686.rpm Wrote: /builddir/build/RPMS/bcftools-1.15.1-2.fc38.i686.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.6y9k3D + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.15.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/bcftools-1.15.1-2.fc38.i386 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.46hWfy + umask 022 + cd /builddir/build/BUILD + rm -rf bcftools-1.15.1 bcftools-1.15.1.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0