Mock Version: 1.4.21 Mock Version: 1.4.21 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64le --nodeps /builddir/build/SPECS/bcftools.spec'], chrootPath='/var/lib/mock/f31-build-18404078-1310166/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=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64le --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'} and shell False Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1574121600 Wrote: /builddir/build/SRPMS/bcftools-1.9-1.fc31.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64le --nodeps /builddir/build/SPECS/bcftools.spec'], chrootPath='/var/lib/mock/f31-build-18404078-1310166/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=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64le --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'} and shell False Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1574121600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.lR5qki + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bcftools-1.9 + /usr/bin/bzip2 -dc /builddir/build/SOURCES/bcftools-1.9.tar.bz2 + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd bcftools-1.9 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (bcftools-1.9-python3.patch): + echo 'Patch #0 (bcftools-1.9-python3.patch):' + /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .py3 --fuzz=0 patching file misc/guess-ploidy.py patching file misc/plot-roh.py Patch #1 (bcftools-1.9-configure.patch): + echo 'Patch #1 (bcftools-1.9-configure.patch):' + /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .conf --fuzz=0 patching file config.mk.in patching file configure.ac patching file configure + 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 python|/usr/bin/python3|' misc/guess-ploidy.py misc/plot-roh.py + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.P71AXj + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.9 + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + export LDFLAGS + '[' 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 + ./configure --build=ppc64le-redhat-linux-gnu --host=ppc64le-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/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' --prefix=/usr --with-htslib=system --enable-perl-filters --enable-libgsl '--with-bcf-plugin-path=/usr/local/libexec/bcftools:$(plugindir)' checking for ppc64le-redhat-linux-gnu-gcc... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /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... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -ldl checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for gsl/gsl_version.h... yes checking for library containing cblas_dgemm... -lgslcblas checking for gsl_multifit_gradient in -lgsl... yes 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 -j4 V=1 VERBOSE=1 echo '#define BCFTOOLS_VERSION "1.9"' > version.h gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfindex.o vcfindex.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o tabix.o tabix.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfisec.o vcfisec.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfquery.o vcfquery.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcffilter.o vcffilter.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfstats.o vcfstats.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfsom.o vcfsom.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfgtcheck.o vcfgtcheck.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfview.o vcfview.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfmerge.o vcfmerge.c vcfmerge.c: In function 'maux_init': vcfmerge.c:682:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 682 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:29, from /usr/include/htslib/vcf.h:40, from vcfmerge.c:31: /usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ vcfmerge.c: In function 'merge_vcf': vcfmerge.c:2334:46: warning: '__builtin___snprintf_chk' output may be truncated before the last format character [-Wformat-truncation=] 2334 | char buf[10]; snprintf(buf,10,"%d",i+1); | ^ In file included from /usr/include/stdio.h:867, from vcfmerge.c:25: /usr/include/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 10 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -D_REENTRANT -D_GNU_SOURCE -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -c -o filter.o filter.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfnorm.o vcfnorm.c In function 'realign', inlined from 'normalize_line' at vcfnorm.c:1717:23: vcfnorm.c:345:17: warning: '%s' directive argument is null [-Wformat-overflow=] 345 | error("Non-ACGTN alternate allele at %s:%d .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),line->pos+1,ref,line->d.allele[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfconcat.o vcfconcat.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfroh.o vcfroh.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfcall.o vcfcall.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcmp.o vcmp.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o gvcf.o gvcf.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfannotate.o vcfannotate.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o reheader.o reheader.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o tsv2vcf.o tsv2vcf.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o mcall.o mcall.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o HMM.o HMM.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfcnv.o vcfcnv.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfconvert.o vcfconvert.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -DPLUGINPATH='"/usr/local/libexec/bcftools:/usr/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bin.o bin.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o hclust.o hclust.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o version.o version.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o consensus.o consensus.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o ploidy.o ploidy.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o smpl_ilist.o smpl_ilist.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfbuf.o vcfbuf.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o convert.o convert.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o regidx.o regidx.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o mpileup.o mpileup.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bam2bcf.o bam2bcf.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o vcfsort.o vcfsort.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o ccall.o ccall.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o em.o em.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o kmin.o kmin.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o prob1.o prob1.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o polysomy.o polysomy.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o bam_sample.o bam_sample.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o test/test-rbuf.o test/test-rbuf.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o test/test-regidx.o test/test-regidx.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o peakfit.o peakfit.c gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -c -o csq.o csq.c gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/split.so version.c plugins/split.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/trio-stats.so version.c plugins/trio-stats.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/counts.so version.c plugins/counts.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -D_REENTRANT -D_GNU_SOURCE -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/setGT.so filter.c version.c plugins/setGT.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/mendelian.so version.c plugins/mendelian.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/contrast.so version.c plugins/contrast.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/impute-info.so version.c plugins/impute-info.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/prune.so version.c plugins/prune.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/fixref.so version.c plugins/fixref.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/dosage.so version.c plugins/dosage.c -ldl gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-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 -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -ldl -ldl gcc -rdynamic -pthread -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o ccall.o em.o prob1.o kmin.o polysomy.o peakfit.o -lhts -lm -lz -ldl -ldl -lgsl -lgslcblas -Wl,--enable-new-dtags -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fstack-protector-strong -L/usr/local/lib -L/usr/lib64/perl5/CORE -lperl -lpthread -lresolv -ldl -lm -lcrypt -lutil -lc gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/GTisec.so version.c plugins/GTisec.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I. -D_REENTRANT -D_GNU_SOURCE -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/CORE -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.ExLSoi + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le ++ dirname /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le + cd bcftools-1.9 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/bin /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/share/man/man1 /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools /usr/bin/install -p bcftools /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/bin /usr/bin/install -p misc/color-chrs.pl misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/bin /usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/share/man/man1 /usr/bin/install -p plugins/*.so /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools + /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.9-1.fc31 --unique-debug-suffix -1.9-1.fc31.ppc64le --unique-debug-src-base bcftools-1.9-1.fc31.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bcftools-1.9 explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/bin/bcftools explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/GTisec.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/ad-bias.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/bin/bcftools explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/GTsubset.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/GTisec.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/ad-bias.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/GTsubset.so explicitly decompress any 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/builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/color-chrs.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/contrast.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/contrast.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/counts.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/counts.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/dosage.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/dosage.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/fill-AN-AC.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/fill-AN-AC.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/fill-from-fasta.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/fill-from-fasta.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/fill-tags.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/fixploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/fill-tags.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/fixploidy.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/fixref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/fixref.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/frameshifts.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/frameshifts.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/guess-ploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/guess-ploidy.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/impute-info.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/impute-info.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/isecGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/isecGT.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/mendelian.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/missing2ref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/mendelian.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/missing2ref.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/prune.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/prune.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/setGT.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/smpl-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/setGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/smpl-stats.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/split.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/split.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/tag2tag.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/tag2tag.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/trio-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/trio-stats.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/trio-switch-rate.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/libexec/bcftools/trio-switch-rate.so original debug info size: 6500kB, size after compression: 6048kB /usr/lib/rpm/sepdebugcrcfix: Updated 29 CRC32s, 0 CRC32s did match. 3920 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/redhat/brp-python-bytecompile /usr/bin/python 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.SiPTmj + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.9 + grep -E '/lib(64)?/libhts\.so\.' + ldd bcftools libhts.so.2 => /lib64/libhts.so.2 (0x00007fff94b00000) + 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= test_usage: bcftools ./test/test.pl: module IO::Pty not found; skipping usage tests test_tabix: tabix /tmp/_I4YCntiuB/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/_I4YCntiuB/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/_I4YCntiuB/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/_I4YCntiuB/merge.a.bcf 1:3000151-3000151 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/_I4YCntiuB/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/_I4YCntiuB/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/_I4YCntiuB/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/_I4YCntiuB/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/_I4YCntiuB/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/_I4YCntiuB/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/_I4YCntiuB/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/_I4YCntiuB/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/_I4YCntiuB/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/_I4YCntiuB/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/_I4YCntiuB/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/_I4YCntiuB/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/_I4YCntiuB/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/_I4YCntiuB/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/_I4YCntiuB/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/_I4YCntiuB/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/_I4YCntiuB/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/_I4YCntiuB/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/_I4YCntiuB/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/_I4YCntiuB/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/_I4YCntiuB/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/_I4YCntiuB/empty.bcf .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.9/bcftools stats -s - /tmp/_I4YCntiuB/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/check.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /builddir/build/BUILD/bcftools-1.9/misc/plot-vcfstats -m /tmp/_I4YCntiuB/check.1.chk /tmp/_I4YCntiuB/check.2.chk /tmp/_I4YCntiuB/check.3.chk /tmp/_I4YCntiuB/check.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.9/bcftools stats -s - /tmp/_I4YCntiuB/stats.a.vcf.gz /tmp/_I4YCntiuB/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.9/bcftools stats -s B /tmp/_I4YCntiuB/stats.a.vcf.gz /tmp/_I4YCntiuB/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.9/bcftools stats -s - /tmp/_I4YCntiuB/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -n =2 /tmp/_I4YCntiuB/isec.a.vcf.gz /tmp/_I4YCntiuB/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -Ob -n =2 /tmp/_I4YCntiuB/isec.a.vcf.gz /tmp/_I4YCntiuB/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/_I4YCntiuB/isec.a.vcf.gz /tmp/_I4YCntiuB/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/_I4YCntiuB/isec.a.vcf.gz /tmp/_I4YCntiuB/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -n =2 -c both /tmp/_I4YCntiuB/isec.a.vcf.gz /tmp/_I4YCntiuB/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -Ob -n =2 -c both /tmp/_I4YCntiuB/isec.a.vcf.gz /tmp/_I4YCntiuB/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -n =2 -c any /tmp/_I4YCntiuB/isec.a.vcf.gz /tmp/_I4YCntiuB/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -Ob -n =2 -c any /tmp/_I4YCntiuB/isec.a.vcf.gz /tmp/_I4YCntiuB/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -C -c any /tmp/_I4YCntiuB/isec.a.vcf.gz /tmp/_I4YCntiuB/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -Ob -C -c any /tmp/_I4YCntiuB/isec.a.vcf.gz /tmp/_I4YCntiuB/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.9/bcftools isec --no-version -T /tmp/_I4YCntiuB/isec.tab.gz /tmp/_I4YCntiuB/isec.a.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.9/bcftools isec -Ob -T /tmp/_I4YCntiuB/isec.tab.gz /tmp/_I4YCntiuB/isec.a.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge --no-version --force-samples /tmp/_I4YCntiuB/merge.a.vcf.gz /tmp/_I4YCntiuB/merge.b.vcf.gz /tmp/_I4YCntiuB/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples /tmp/_I4YCntiuB/merge.a.vcf.gz /tmp/_I4YCntiuB/merge.b.vcf.gz /tmp/_I4YCntiuB/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge --no-version --force-samples -Fx /tmp/_I4YCntiuB/merge.a.vcf.gz /tmp/_I4YCntiuB/merge.b.vcf.gz /tmp/_I4YCntiuB/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -Fx /tmp/_I4YCntiuB/merge.a.vcf.gz /tmp/_I4YCntiuB/merge.b.vcf.gz /tmp/_I4YCntiuB/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge --no-version --force-samples -0 /tmp/_I4YCntiuB/merge.a.vcf.gz /tmp/_I4YCntiuB/merge.b.vcf.gz /tmp/_I4YCntiuB/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -0 /tmp/_I4YCntiuB/merge.a.vcf.gz /tmp/_I4YCntiuB/merge.b.vcf.gz /tmp/_I4YCntiuB/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge --no-version --force-samples -m none /tmp/_I4YCntiuB/merge.2.a.vcf.gz /tmp/_I4YCntiuB/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -m none /tmp/_I4YCntiuB/merge.2.a.vcf.gz /tmp/_I4YCntiuB/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge --no-version --force-samples -m both /tmp/_I4YCntiuB/merge.2.a.vcf.gz /tmp/_I4YCntiuB/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -m both /tmp/_I4YCntiuB/merge.2.a.vcf.gz /tmp/_I4YCntiuB/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge --no-version --force-samples -m all /tmp/_I4YCntiuB/merge.2.a.vcf.gz /tmp/_I4YCntiuB/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -m all /tmp/_I4YCntiuB/merge.2.a.vcf.gz /tmp/_I4YCntiuB/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/_I4YCntiuB/merge.3.a.vcf.gz /tmp/_I4YCntiuB/merge.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/_I4YCntiuB/merge.3.a.vcf.gz /tmp/_I4YCntiuB/merge.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge --no-version --force-samples -m id /tmp/_I4YCntiuB/merge.4.a.vcf.gz /tmp/_I4YCntiuB/merge.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -m id /tmp/_I4YCntiuB/merge.4.a.vcf.gz /tmp/_I4YCntiuB/merge.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge --no-version --gvcf - /tmp/_I4YCntiuB/gvcf.merge.1.vcf.gz /tmp/_I4YCntiuB/gvcf.merge.2.vcf.gz /tmp/_I4YCntiuB/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/_I4YCntiuB/gvcf.merge.1.vcf.gz /tmp/_I4YCntiuB/gvcf.merge.2.vcf.gz /tmp/_I4YCntiuB/gvcf.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge --no-version --gvcf - /tmp/_I4YCntiuB/merge.gvcf.2.a.vcf.gz /tmp/_I4YCntiuB/merge.gvcf.2.b.vcf.gz /tmp/_I4YCntiuB/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/_I4YCntiuB/merge.gvcf.2.a.vcf.gz /tmp/_I4YCntiuB/merge.gvcf.2.b.vcf.gz /tmp/_I4YCntiuB/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge --no-version --gvcf - -i SRC:join /tmp/_I4YCntiuB/merge.gvcf.3.a.vcf.gz /tmp/_I4YCntiuB/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --gvcf - -i SRC:join /tmp/_I4YCntiuB/merge.gvcf.3.a.vcf.gz /tmp/_I4YCntiuB/merge.gvcf.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge --no-version /tmp/_I4YCntiuB/merge.5.a.vcf.gz /tmp/_I4YCntiuB/merge.5.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob /tmp/_I4YCntiuB/merge.5.a.vcf.gz /tmp/_I4YCntiuB/merge.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/_I4YCntiuB/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/_I4YCntiuB/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/_I4YCntiuB/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/_I4YCntiuB/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/_I4YCntiuB/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/_I4YCntiuB/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/_I4YCntiuB/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/_I4YCntiuB/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/_I4YCntiuB/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/_I4YCntiuB/view.vectors.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/_I4YCntiuB/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/_I4YCntiuB/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/_I4YCntiuB/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/_I4YCntiuB/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/_I4YCntiuB/query.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.2.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%LINE' /tmp/_I4YCntiuB/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%LINE' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/_I4YCntiuB/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/_I4YCntiuB/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/_I4YCntiuB/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/_I4YCntiuB/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/_I4YCntiuB/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/_I4YCntiuB/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/_I4YCntiuB/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/_I4YCntiuB/query.filter.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter.2.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/_I4YCntiuB/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/_I4YCntiuB/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/_I4YCntiuB/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/_I4YCntiuB/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/_I4YCntiuB/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/_I4YCntiuB/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/_I4YCntiuB/query.filter.4.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter.4.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.9/test/query.56.out' /tmp/_I4YCntiuB/view.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.9/test/query.56.out' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/_I4YCntiuB/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/_I4YCntiuB/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/_I4YCntiuB/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -cx -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa /tmp/_I4YCntiuB/norm.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -cx -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa /tmp/_I4YCntiuB/norm.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -m- /tmp/_I4YCntiuB/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m- /tmp/_I4YCntiuB/norm.split.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -m- /tmp/_I4YCntiuB/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m- /tmp/_I4YCntiuB/norm.split.2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -m- -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa /tmp/_I4YCntiuB/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m- -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa /tmp/_I4YCntiuB/norm.split.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -m+ /tmp/_I4YCntiuB/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m+ /tmp/_I4YCntiuB/norm.merge.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -m+ /tmp/_I4YCntiuB/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m+ /tmp/_I4YCntiuB/norm.merge.2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -m+ /tmp/_I4YCntiuB/norm.merge.3.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m+ /tmp/_I4YCntiuB/norm.merge.3.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ [W::bcf_hdr_register_hrec] An INFO field has no Number defined. Assuming '.' .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -m+ -s /tmp/_I4YCntiuB/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m+ -s /tmp/_I4YCntiuB/norm.merge.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -Nc s -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa /tmp/_I4YCntiuB/norm.setref.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -Nc s -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa /tmp/_I4YCntiuB/norm.setref.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa /tmp/_I4YCntiuB/norm.telomere.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa /tmp/_I4YCntiuB/norm.telomere.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -d snps /tmp/_I4YCntiuB/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d snps /tmp/_I4YCntiuB/norm.rmdup.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -d indels /tmp/_I4YCntiuB/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d indels /tmp/_I4YCntiuB/norm.rmdup.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -d both /tmp/_I4YCntiuB/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d both /tmp/_I4YCntiuB/norm.rmdup.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -d all /tmp/_I4YCntiuB/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d all /tmp/_I4YCntiuB/norm.rmdup.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm --no-version -d none /tmp/_I4YCntiuB/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d none /tmp/_I4YCntiuB/norm.rmdup.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/_I4YCntiuB/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/_I4YCntiuB/view.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -f PASS -Xks NA00003 /tmp/_I4YCntiuB/view.vcf.gz -r20,Y .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -f PASS -Xks NA00003 /tmp/_I4YCntiuB/view.vcf.gz -r20,Y | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -xs NA00003 /tmp/_I4YCntiuB/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -xs NA00003 /tmp/_I4YCntiuB/view.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/_I4YCntiuB/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/_I4YCntiuB/view.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -p /tmp/_I4YCntiuB/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -p /tmp/_I4YCntiuB/view.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -P /tmp/_I4YCntiuB/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -P /tmp/_I4YCntiuB/view.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/_I4YCntiuB/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/_I4YCntiuB/view.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -Hu /tmp/_I4YCntiuB/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -GVsnps /tmp/_I4YCntiuB/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -GVsnps /tmp/_I4YCntiuB/view.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/_I4YCntiuB/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/_I4YCntiuB/view.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -s ^NA00003 /tmp/_I4YCntiuB/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -s ^NA00003 /tmp/_I4YCntiuB/view.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version /tmp/_I4YCntiuB/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -G /tmp/_I4YCntiuB/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -G /tmp/_I4YCntiuB/view.omitgenotypes.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -HG /tmp/_I4YCntiuB/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -a /tmp/_I4YCntiuB/many.alleles.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -a /tmp/_I4YCntiuB/many.alleles.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -asA /tmp/_I4YCntiuB/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -asA /tmp/_I4YCntiuB/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -asB /tmp/_I4YCntiuB/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -asB /tmp/_I4YCntiuB/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -asA /tmp/_I4YCntiuB/view.vectors.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -asA /tmp/_I4YCntiuB/view.vectors.2.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -i'TXT0="text"' /tmp/_I4YCntiuB/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.9/test/view.chrs.tab /tmp/_I4YCntiuB/view.chrs.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.9/test/view.chrs.tab /tmp/_I4YCntiuB/view.chrs.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -i 'POS>=3062917' /tmp/_I4YCntiuB/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -i 'POS>=3062917' /tmp/_I4YCntiuB/filter.2.vcf.gz 1:3062917-3157410 | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.9/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.9/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.9/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.9/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.9/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.9/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.9/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -C5:nonmajor /tmp/_I4YCntiuB/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -c6:nonmajor /tmp/_I4YCntiuB/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -q0.3:major /tmp/_I4YCntiuB/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/_I4YCntiuB/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/_I4YCntiuB/view.filter.annovar.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/_I4YCntiuB/view.filter.annovar.vcf.gz .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.9/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.9/test/mpileup.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call --no-version -mg0 /builddir/build/BUILD/bcftools-1.9/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call -Ob -mg0 /builddir/build/BUILD/bcftools-1.9/test/mpileup.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.9/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.9/test/mpileup.samples /builddir/build/BUILD/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.9/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.9/test/mpileup.samples /builddir/build/BUILD/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.9/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.9/test/mpileup.ped /builddir/build/BUILD/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.9/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.9/test/mpileup.ped /builddir/build/BUILD/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.9/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.9/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.9/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.9/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.9/test/mpileup.X.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.9/bcftools call --no-version -mA -C alleles -T /tmp/_I4YCntiuB/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.9/test/mpileup.vcf 2>/dev/null .. ok test_vcf_call_cAls: /builddir/build/BUILD/bcftools-1.9/bcftools call -Ob -mA -C alleles -T /tmp/_I4YCntiuB/mpileup.tab.gz /builddir/build/BUILD/bcftools-1.9/test/mpileup.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call --no-version -cv /builddir/build/BUILD/bcftools-1.9/test/mpileup.c.vcf 2>/dev/null .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call -Ob -cv /builddir/build/BUILD/bcftools-1.9/test/mpileup.c.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.9/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.9/test/mpileup.samples /builddir/build/BUILD/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.9/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.9/test/mpileup.samples /builddir/build/BUILD/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.9/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.9/test/mpileup.ped /builddir/build/BUILD/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.9/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.9/test/mpileup.ped /builddir/build/BUILD/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.9/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.9/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null .. ok test_vcf_call: /builddir/build/BUILD/bcftools-1.9/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.9/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.9/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.9/test/mpileup.c.X.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.9/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.9/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.9/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'ALT="."' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'ALT="."' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.9/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.9/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.9/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.9/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'GT="A"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'GT="A"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'GT="RR"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'GT="RR"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'GT="RA"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'GT="RA"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'GT="AR"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'GT="AR"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'GT="AA"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'GT="AA"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'GT="aA"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'GT="aA"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'GT="HET"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'GT="HET"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.9/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /builddir/build/BUILD/bcftools-1.9/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.9/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.9/bcftools sort -m 0 /builddir/build/BUILD/bcftools-1.9/test/sort.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.3mkSI5 Merging 17 temporary files Cleaning Done .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.9/bcftools sort -Ob -m 0 /builddir/build/BUILD/bcftools-1.9/test/sort.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.vu660j Merging 17 temporary files Cleaning Done .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.9/bcftools sort -m 1000 /builddir/build/BUILD/bcftools-1.9/test/sort.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.LqVtvB Merging 5 temporary files Cleaning Done .. ok test_vcf_sort: /builddir/build/BUILD/bcftools-1.9/bcftools sort -Ob -m 1000 /builddir/build/BUILD/bcftools-1.9/test/sort.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | /builddir/build/BUILD/bcftools-1.9/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' Writing to /tmp/bcftools-sort.LHzcBQ Merging 5 temporary files Cleaning Done .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.9/test/regions.tab /tmp/_I4YCntiuB/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.9/test/regions.tab .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /builddir/build/BUILD/bcftools-1.9/test/regions.tab /tmp/_I4YCntiuB/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/_I4YCntiuB/regions.tab.gz /tmp/_I4YCntiuB/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/_I4YCntiuB/regions.tab.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/_I4YCntiuB/regions.tab.gz /tmp/_I4YCntiuB/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/_I4YCntiuB/regions.bed /tmp/_I4YCntiuB/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/_I4YCntiuB/regions.bed .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/_I4YCntiuB/regions.bed /tmp/_I4YCntiuB/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/_I4YCntiuB/regions.bed.gz /tmp/_I4YCntiuB/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/_I4YCntiuB/regions.bed.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/_I4YCntiuB/regions.bed.gz /tmp/_I4YCntiuB/regions.vcf.gz .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.9/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.9/test/annotate.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.9/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.9/test/annotate.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.9/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.9/test/annotate.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.9/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.9/test/annotate.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/_I4YCntiuB/annotate.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/_I4YCntiuB/annotate.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/_I4YCntiuB/annotate2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/_I4YCntiuB/annotate2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/_I4YCntiuB/annotate2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/_I4YCntiuB/annotate2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.9/test/annotate3.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.9/test/annotate3.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -x FORMAT /builddir/build/BUILD/bcftools-1.9/test/annotate3.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -x FORMAT /builddir/build/BUILD/bcftools-1.9/test/annotate3.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annots4.vcf.gz -c +INFO /tmp/_I4YCntiuB/annotate4.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annots4.vcf.gz -c +INFO /tmp/_I4YCntiuB/annotate4.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.9/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.9/test/annotate4.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.9/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.9/test/annotate4.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.9/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.9/test/annotate10.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.9/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.9/test/annotate10.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/_I4YCntiuB/annotate2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/_I4YCntiuB/annotate2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.9/test/annotate2.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.9/test/annotate2.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/_I4YCntiuB/annotate2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/_I4YCntiuB/annotate2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/_I4YCntiuB/annotate2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/_I4YCntiuB/annotate2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/_I4YCntiuB/annotate2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/_I4YCntiuB/annotate2.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annots11.vcf.gz -c FMT /tmp/_I4YCntiuB/annotate11.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annots11.vcf.gz -c FMT /tmp/_I4YCntiuB/annotate11.vcf.gz 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +missing2ref --no-version /tmp/_I4YCntiuB/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +missing2ref --no-version /tmp/_I4YCntiuB/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +setGT --no-version /tmp/_I4YCntiuB/plugin1.vcf.gz -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +setGT --no-version /tmp/_I4YCntiuB/plugin1.bcf -- -t . -n 0 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +setGT --no-version /tmp/_I4YCntiuB/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +setGT --no-version /tmp/_I4YCntiuB/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +setGT --no-version /tmp/_I4YCntiuB/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.9/test/setGT.samples.txt]="het"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +setGT --no-version /tmp/_I4YCntiuB/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.9/test/setGT.samples.txt]="het"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +setGT --no-version /tmp/_I4YCntiuB/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.9/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.9/test/setGT.samples.txt])<0.1' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +setGT --no-version /tmp/_I4YCntiuB/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.9/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.9/test/setGT.samples.txt])<0.1' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/_I4YCntiuB/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.9/test/annotate9.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -Ob -a /tmp/_I4YCntiuB/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.9/test/annotate9.vcf 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-AN-AC --no-version /tmp/_I4YCntiuB/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-AN-AC --no-version /tmp/_I4YCntiuB/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +dosage /tmp/_I4YCntiuB/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +dosage /tmp/_I4YCntiuB/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fixploidy --no-version /tmp/_I4YCntiuB/fixploidy.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.9/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.9/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fixploidy --no-version /tmp/_I4YCntiuB/fixploidy.bcf -- -s /builddir/build/BUILD/bcftools-1.9/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.9/test/fixploidy.ploidy 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +guess-ploidy /tmp/_I4YCntiuB/view.PL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +guess-ploidy /tmp/_I4YCntiuB/view.PL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +guess-ploidy /tmp/_I4YCntiuB/view.GL.vcf.gz -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ Warning: PL tag not found in header, switching to GL .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +guess-ploidy /tmp/_I4YCntiuB/view.GL.bcf -vrX | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ Warning: PL tag not found in header, switching to GL .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +tag2tag --no-version /tmp/_I4YCntiuB/view.GL.vcf.gz -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +tag2tag --no-version /tmp/_I4YCntiuB/view.GL.bcf -- -r --gl-to-pl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +tag2tag --no-version /tmp/_I4YCntiuB/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +tag2tag --no-version /tmp/_I4YCntiuB/view.GP.bcf -- -r --gp-to-gt -t 0.2 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-tags --no-version /tmp/_I4YCntiuB/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-tags --no-version /tmp/_I4YCntiuB/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-tags --no-version /tmp/_I4YCntiuB/view.vcf.gz -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-tags --no-version /tmp/_I4YCntiuB/view.bcf -- -t AC,AN,AF,MAF,NS 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-tags --no-version /tmp/_I4YCntiuB/view.vcf.gz -- -t AC -S /builddir/build/BUILD/bcftools-1.9/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-tags --no-version /tmp/_I4YCntiuB/view.bcf -- -t AC -S /builddir/build/BUILD/bcftools-1.9/test/fill-tags.3.smpl 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-tags --no-version /tmp/_I4YCntiuB/fill-tags-hemi.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-tags --no-version /tmp/_I4YCntiuB/fill-tags-hemi.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-tags --no-version /tmp/_I4YCntiuB/fill-tags-hemi.vcf.gz -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-tags --no-version /tmp/_I4YCntiuB/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.vcf.gz -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.bcf -- -H | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.vcf.gz -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.bcf -- -Hm | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.vcf.gz -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.bcf -- -Hmv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.vcf.gz -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.bcf -- -Hv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.vcf.gz -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.bcf -- -m | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.vcf.gz -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.bcf -- -mv | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.vcf.gz -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/_I4YCntiuB/view.bcf -- -v | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +trio-switch-rate /tmp/_I4YCntiuB/trio.vcf.gz -- -p /builddir/build/BUILD/bcftools-1.9/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +trio-switch-rate /tmp/_I4YCntiuB/trio.bcf -- -p /builddir/build/BUILD/bcftools-1.9/test/trio.ped | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +trio-stats /tmp/_I4YCntiuB/trio-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.9/test/trio-stats.ped | grep -v ^CMD 2>/dev/null | grep -v ^##bcftools_ Identified 2 complete trios in the VCF file .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +trio-stats /tmp/_I4YCntiuB/trio-stats.bcf -p /builddir/build/BUILD/bcftools-1.9/test/trio-stats.ped | grep -v ^CMD 2>/dev/null | grep -v ^##bcftools_ Identified 2 complete trios in the VCF file .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +ad-bias /tmp/_I4YCntiuB/ad-bias.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.9/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +ad-bias /tmp/_I4YCntiuB/ad-bias.bcf -- -s /builddir/build/BUILD/bcftools-1.9/test/ad-bias.samples | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +af-dist /tmp/_I4YCntiuB/af-dist.vcf.gz | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +af-dist /tmp/_I4YCntiuB/af-dist.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fixref /tmp/_I4YCntiuB/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa -i /tmp/_I4YCntiuB/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fixref /tmp/_I4YCntiuB/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa -i /tmp/_I4YCntiuB/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fixref /tmp/_I4YCntiuB/fixref.3.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.9/test/fixref.3.fa -m top 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fixref /tmp/_I4YCntiuB/fixref.3.bcf -- -f /builddir/build/BUILD/bcftools-1.9/test/fixref.3.fa -m top 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-from-fasta /tmp/_I4YCntiuB/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.9/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.9/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-from-fasta /tmp/_I4YCntiuB/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.9/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.9/test/aa.hdr -i 'TYPE="snp"' 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-from-fasta /tmp/_I4YCntiuB/ref.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fill-from-fasta /tmp/_I4YCntiuB/ref.bcf -- -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa -c REF 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTsubset --no-version /tmp/_I4YCntiuB/view.vcf.gz -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTsubset --no-version /tmp/_I4YCntiuB/view.bcf -- -s NA00001 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTsubset --no-version /tmp/_I4YCntiuB/view.vcf.gz -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTsubset --no-version /tmp/_I4YCntiuB/view.bcf -- -s NA00001,NA00002 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTsubset --no-version /tmp/_I4YCntiuB/view.vcf.gz -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTsubset --no-version /tmp/_I4YCntiuB/view.bcf -- -s NA00001,NA00002,NA00003 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +mendelian /tmp/_I4YCntiuB/mendelian.vcf.gz -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +mendelian /tmp/_I4YCntiuB/mendelian.bcf -t mom1,dad1,child1 -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +mendelian /tmp/_I4YCntiuB/mendelian.vcf.gz -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +mendelian /tmp/_I4YCntiuB/mendelian.bcf -t mom1,dad1,child1 -l+ 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +mendelian /tmp/_I4YCntiuB/mendelian.vcf.gz -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +mendelian /tmp/_I4YCntiuB/mendelian.bcf -t mom1,dad1,child1 -lx 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +contrast /tmp/_I4YCntiuB/contrast.vcf.gz -0 a,b -1 c 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +contrast /tmp/_I4YCntiuB/contrast.bcf -0 a,b -1 c 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat --no-version /tmp/_I4YCntiuB/concat.1.a.vcf.gz /tmp/_I4YCntiuB/concat.1.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob /tmp/_I4YCntiuB/concat.1.a.vcf.gz /tmp/_I4YCntiuB/concat.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat --no-version /tmp/_I4YCntiuB/concat.1.a.bcf /tmp/_I4YCntiuB/concat.1.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob /tmp/_I4YCntiuB/concat.1.a.bcf /tmp/_I4YCntiuB/concat.1.b.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat --no-version -a /tmp/_I4YCntiuB/concat.2.a.vcf.gz /tmp/_I4YCntiuB/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -a /tmp/_I4YCntiuB/concat.2.a.vcf.gz /tmp/_I4YCntiuB/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat --no-version -a /tmp/_I4YCntiuB/concat.2.a.bcf /tmp/_I4YCntiuB/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -a /tmp/_I4YCntiuB/concat.2.a.bcf /tmp/_I4YCntiuB/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat --no-version -aD /tmp/_I4YCntiuB/concat.2.a.vcf.gz /tmp/_I4YCntiuB/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -aD /tmp/_I4YCntiuB/concat.2.a.vcf.gz /tmp/_I4YCntiuB/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat --no-version -aD /tmp/_I4YCntiuB/concat.2.a.bcf /tmp/_I4YCntiuB/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -aD /tmp/_I4YCntiuB/concat.2.a.bcf /tmp/_I4YCntiuB/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat --no-version -l /tmp/_I4YCntiuB/concat.3.a.vcf.gz /tmp/_I4YCntiuB/concat.3.b.vcf.gz /tmp/_I4YCntiuB/concat.3.0.vcf.gz /tmp/_I4YCntiuB/concat.3.c.vcf.gz /tmp/_I4YCntiuB/concat.3.d.vcf.gz /tmp/_I4YCntiuB/concat.3.e.vcf.gz /tmp/_I4YCntiuB/concat.3.f.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -l /tmp/_I4YCntiuB/concat.3.a.vcf.gz /tmp/_I4YCntiuB/concat.3.b.vcf.gz /tmp/_I4YCntiuB/concat.3.0.vcf.gz /tmp/_I4YCntiuB/concat.3.c.vcf.gz /tmp/_I4YCntiuB/concat.3.d.vcf.gz /tmp/_I4YCntiuB/concat.3.e.vcf.gz /tmp/_I4YCntiuB/concat.3.f.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat --no-version -l /tmp/_I4YCntiuB/concat.3.a.bcf /tmp/_I4YCntiuB/concat.3.b.bcf /tmp/_I4YCntiuB/concat.3.0.bcf /tmp/_I4YCntiuB/concat.3.c.bcf /tmp/_I4YCntiuB/concat.3.d.bcf /tmp/_I4YCntiuB/concat.3.e.bcf /tmp/_I4YCntiuB/concat.3.f.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -l /tmp/_I4YCntiuB/concat.3.a.bcf /tmp/_I4YCntiuB/concat.3.b.bcf /tmp/_I4YCntiuB/concat.3.0.bcf /tmp/_I4YCntiuB/concat.3.c.bcf /tmp/_I4YCntiuB/concat.3.d.bcf /tmp/_I4YCntiuB/concat.3.e.bcf /tmp/_I4YCntiuB/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1638025819 .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat --naive /tmp/_I4YCntiuB/naive_concat.0.bcf /tmp/_I4YCntiuB/naive_concat.1.bcf /tmp/_I4YCntiuB/naive_concat.2.bcf /tmp/_I4YCntiuB/naive_concat.3.bcf /tmp/_I4YCntiuB/naive_concat.4.bcf /tmp/_I4YCntiuB/naive_concat.5.bcf /tmp/_I4YCntiuB/naive_concat.6.bcf /tmp/_I4YCntiuB/naive_concat.7.bcf /tmp/_I4YCntiuB/naive_concat.8.bcf /tmp/_I4YCntiuB/naive_concat.9.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view -H .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat --naive /tmp/_I4YCntiuB/naive_concat.0.vcf.gz /tmp/_I4YCntiuB/naive_concat.1.vcf.gz /tmp/_I4YCntiuB/naive_concat.2.vcf.gz /tmp/_I4YCntiuB/naive_concat.3.vcf.gz /tmp/_I4YCntiuB/naive_concat.4.vcf.gz /tmp/_I4YCntiuB/naive_concat.5.vcf.gz /tmp/_I4YCntiuB/naive_concat.6.vcf.gz /tmp/_I4YCntiuB/naive_concat.7.vcf.gz /tmp/_I4YCntiuB/naive_concat.8.vcf.gz /tmp/_I4YCntiuB/naive_concat.9.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view -H .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -h /builddir/build/BUILD/bcftools-1.9/test/reheader.hdr /builddir/build/BUILD/bcftools-1.9/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.9/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -h /builddir/build/BUILD/bcftools-1.9/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -h /builddir/build/BUILD/bcftools-1.9/test/reheader.hdr /tmp/_I4YCntiuB/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/_I4YCntiuB/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -h /builddir/build/BUILD/bcftools-1.9/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -h /builddir/build/BUILD/bcftools-1.9/test/reheader.hdr /tmp/_I4YCntiuB/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/_I4YCntiuB/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -h /builddir/build/BUILD/bcftools-1.9/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples /builddir/build/BUILD/bcftools-1.9/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.9/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples /tmp/_I4YCntiuB/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/_I4YCntiuB/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples /tmp/_I4YCntiuB/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/_I4YCntiuB/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples2 /builddir/build/BUILD/bcftools-1.9/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.9/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples2 /tmp/_I4YCntiuB/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/_I4YCntiuB/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples2 /tmp/_I4YCntiuB/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/_I4YCntiuB/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples3 /builddir/build/BUILD/bcftools-1.9/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.9/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples3 /tmp/_I4YCntiuB/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/_I4YCntiuB/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples3 /tmp/_I4YCntiuB/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/_I4YCntiuB/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples4 /builddir/build/BUILD/bcftools-1.9/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.9/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples4 /tmp/_I4YCntiuB/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/_I4YCntiuB/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples4 /tmp/_I4YCntiuB/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/_I4YCntiuB/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -s /builddir/build/BUILD/bcftools-1.9/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -h /builddir/build/BUILD/bcftools-1.9/test/reheader.empty.hdr /builddir/build/BUILD/bcftools-1.9/test/empty.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /builddir/build/BUILD/bcftools-1.9/test/empty.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -h /builddir/build/BUILD/bcftools-1.9/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -h /builddir/build/BUILD/bcftools-1.9/test/reheader.empty.hdr /tmp/_I4YCntiuB/empty.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/_I4YCntiuB/empty.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -h /builddir/build/BUILD/bcftools-1.9/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: /builddir/build/BUILD/bcftools-1.9/bcftools reheader -h /builddir/build/BUILD/bcftools-1.9/test/reheader.empty.hdr /tmp/_I4YCntiuB/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/_I4YCntiuB/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools reheader -h /builddir/build/BUILD/bcftools-1.9/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.9/bcftools annotate --rename-chrs /tmp/_I4YCntiuB/rename.map -Ov /tmp/_I4YCntiuB/annotate.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.9/bcftools annotate --rename-chrs /tmp/_I4YCntiuB/rename.map -Ob /tmp/_I4YCntiuB/annotate.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.9/bcftools annotate --rename-chrs /tmp/_I4YCntiuB/rename.map -Ov /builddir/build/BUILD/bcftools-1.9/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /builddir/build/BUILD/bcftools-1.9/bcftools annotate --rename-chrs /tmp/_I4YCntiuB/rename.map -Ob /builddir/build/BUILD/bcftools-1.9/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert -g -,. /tmp/_I4YCntiuB/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert -g -,. 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert -g .,- /tmp/_I4YCntiuB/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert -g .,- 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert -g -,. --tag PL /tmp/_I4YCntiuB/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert -g -,. --tag PL 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert -g .,- --tag PL /tmp/_I4YCntiuB/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert -g .,- --tag PL 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert -g -,. --vcf-ids /tmp/_I4YCntiuB/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/check.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert -g -,. --vcf-ids 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert -g .,- --vcf-ids /tmp/_I4YCntiuB/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/check.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert -g .,- --vcf-ids 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert -g -,. --chrom /tmp/_I4YCntiuB/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/check.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert -g -,. --chrom 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert -g .,- --chrom /tmp/_I4YCntiuB/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/check.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert -g .,- --chrom 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert -g -,. --chrom --vcf-ids /tmp/_I4YCntiuB/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/check.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert -g -,. --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert -g .,- --chrom --vcf-ids /tmp/_I4YCntiuB/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/check.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert -g .,- --chrom --vcf-ids 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert -h -,.,. /tmp/_I4YCntiuB/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert -h -,.,. 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert -h .,-,. /tmp/_I4YCntiuB/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert -h .,-,. 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert -h .,.,- /tmp/_I4YCntiuB/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert -h .,.,- 2>/dev/null .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.9/bcftools convert -H /builddir/build/BUILD/bcftools-1.9/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.9/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.9/test/convert.hls.gt.samples 2>/dev/null | grep -v ^## .. ok test_vcf_convert_hls2vcf: /builddir/build/BUILD/bcftools-1.9/bcftools convert -H /builddir/build/BUILD/bcftools-1.9/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.9/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.9/test/convert.hls.gt.samples -Ou 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.9/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.9/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.9/test/convert.hs.gt.samples 2>/dev/null | grep -v ^## .. ok test_vcf_convert_hs2vcf: /builddir/build/BUILD/bcftools-1.9/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.9/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.9/test/convert.hs.gt.samples -Ou 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^## .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert --hapsample -,. /tmp/_I4YCntiuB/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert --hapsample -,. 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert --hapsample .,- /tmp/_I4YCntiuB/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert --hapsample .,- 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools convert --haplegendsample -,.,. /tmp/_I4YCntiuB/convert.hap-missing.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/convert.hap-missing.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert --haplegendsample -,.,. 2>/dev/null .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.9/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.9/test/gvcf.fa /tmp/_I4YCntiuB/convert.gvcf.vcf.gz 2>/dev/null .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/_I4YCntiuB/convert.gvcf.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.9/test/gvcf.fa 2>/dev/null | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.9/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.9/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.9/test/convert.23andme 2>/dev/null .. ok test_vcf_convert_tsv2vcf: /builddir/build/BUILD/bcftools-1.9/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.9/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.9/test/convert.23andme 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/_I4YCntiuB/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.9/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/_I4YCntiuB/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus.fa -m /builddir/build/BUILD/bcftools-1.9/test/consensus.tab -c /tmp/_I4YCntiuB/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/_I4YCntiuB/consensus.1.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/_I4YCntiuB/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.9/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/_I4YCntiuB/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.9/test/consensus.tab -c /tmp/_I4YCntiuB/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/_I4YCntiuB/consensus.2.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/_I4YCntiuB/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.9/test/consensus.tab 2>/dev/null .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/_I4YCntiuB/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.9/test/consensus.tab -c /tmp/_I4YCntiuB/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/_I4YCntiuB/consensus.3.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/_I4YCntiuB/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus.fa -H 1 2>/dev/null .. ok test_vcf_consensus_chain: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/_I4YCntiuB/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus.fa -H 1 -c /tmp/_I4YCntiuB/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/_I4YCntiuB/consensus.4.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/_I4YCntiuB/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus2.fa -H 1 2>/dev/null .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/_I4YCntiuB/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus2.fa -H 2 2>/dev/null .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/_I4YCntiuB/empty.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus.fa 2>/dev/null .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/_I4YCntiuB/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus2.fa -H 2 -M "?" 2>/dev/null .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -b /tmp/_I4YCntiuB/mpileup.bam.list --no-version 2>/dev/null | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob -b /tmp/_I4YCntiuB/mpileup.bam.urllist 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -b /tmp/_I4YCntiuB/mpileup.cram.list --no-version 2>/dev/null | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob -b /tmp/_I4YCntiuB/mpileup.cram.urllist 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.9/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.9/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.9/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.9/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.9/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.9/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.9/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.9/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.9/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.9/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.9/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.9/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.9/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.9/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.9/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.9/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.9/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.9/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.9/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.9/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.9/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.9/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.9/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.9/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.9/test/mpileup/mpileup.4.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/indel-AD.1.bam 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/indel-AD.1.bam 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.9/test/mpileup/indel-AD.1.cram 2>/dev/null | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /builddir/build/BUILD/bcftools-1.9/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.9/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.9/test/mpileup/indel-AD.1.cram 2>/dev/null | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq.gff3 /builddir/build/BUILD/bcftools-1.9/test/csq.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq.gff3 ... Indexed 4 transcripts, 10 exons, 10 CDSs, 6 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000301246/ENST00000301246.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000301246/ENST00000301246.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000301246/15bp-insert.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000301246/ENST00000301246.gff ... Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000256452/ENST00000256452.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000256452/ENST00000256452.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000256452/intron.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000256452/ENST00000256452.gff ... Indexed 1 transcripts, 13 exons, 10 CDSs, 5 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.gff ... Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000295641/ENST00000295641.gff ... Indexed 1 transcripts, 25 exons, 25 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000593942/ENST00000593942.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000593942/ENST00000593942.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000593942/last-codon-deletion.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000593942/ENST00000593942.gff ... Indexed 1 transcripts, 7 exons, 4 CDSs, 5 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.gff ... Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000542803/ENST00000542803.gff ... Indexed 1 transcripts, 9 exons, 8 CDSs, 3 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000382647/ENST00000382647.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000382647/ENST00000382647.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000382647/ENST00000382647.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000357367/ENST00000357367.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000357367/ENST00000357367.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000357367/stop-retained.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000357367/ENST00000357367.gff ... Indexed 1 transcripts, 4 exons, 3 CDSs, 3 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.gff ... Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000573314/ENST00000573314.gff ... Indexed 1 transcripts, 12 exons, 1 CDSs, 13 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000303039/ENST00000303039.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.gff ... Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000318249/ENST00000318249.gff ... Indexed 1 transcripts, 15 exons, 14 CDSs, 3 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000423372/ENST00000423372.gff ... Indexed 1 transcripts, 2 exons, 1 CDSs, 3 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.gff ... Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000479739/ENST00000479739.gff ... Indexed 1 transcripts, 11 exons, 4 CDSs, 9 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000375992/ENST00000375992.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000375992/ENST00000375992.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000375992/ENST00000375992.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000520795/ENST00000520795.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000536784/ENST00000536784.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000410009/ENST00000410009.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000410009/ENST00000410009.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000410009/frameshift.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000410009/ENST00000410009.gff ... Indexed 1 transcripts, 6 exons, 6 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000519442/ENST00000519442.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000519442/ENST00000519442.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000519442/synon-splice-region-del.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000519442/ENST00000519442.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000528237/ENST00000528237.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000528237/ENST00000528237.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000528237/ENST00000528237.gff ... Indexed 1 transcripts, 7 exons, 6 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000381157/ENST00000381157.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000381157/ENST00000381157.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000381157/haploid-diploid.vcf | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000381157/ENST00000381157.gff ... Indexed 1 transcripts, 6 exons, 6 CDSs, 0 UTRs Calling... Warning: Skipping site with non-diploid/non-haploid genotypes at X:31180 C>T .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000545279/ENST00000545279.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000545279/ENST00000545279.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000545279/splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000545279/ENST00000545279.gff ... Indexed 1 transcripts, 9 exons, 7 CDSs, 4 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000420670/start-stop-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000420670/ENST00000420670.gff ... Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000557788/ENST00000557788.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000557788/ENST00000557788.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000557788/long-overlap-del.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000557788/ENST00000557788.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000543077/ENST00000543077.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENSG00000173376/ENSG00000173376.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENSG00000173376/ENSG00000173376.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENSG00000173376/synon.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENSG00000173376/ENSG00000173376.gff ... Indexed 2 transcripts, 8 exons, 6 CDSs, 5 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000409523/ENST00000409523.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000409523/ENST00000409523.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000409523/long-overlapping-del.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000409523/ENST00000409523.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 3 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000218032/start-lost-del.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000218032/ENST00000218032.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000329454/ENST00000329454.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.gff ... Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000373833/ENST00000373833.gff ... Indexed 1 transcripts, 13 exons, 9 CDSs, 6 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000271583/ENST00000271583.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000271583/ENST00000271583.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000271583/splice-acceptor.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000271583/ENST00000271583.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000390520/ENST00000390520.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000390520/ENST00000390520.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000390520/deletion-overlap.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000390520/ENST00000390520.gff ... Indexed 1 transcripts, 1 exons, 1 CDSs, 0 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000624631/ENST00000624631.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000624631/ENST00000624631.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000624631/ambiguous.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000624631/ENST00000624631.gff ... Indexed 1 transcripts, 3 exons, 3 CDSs, 0 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000378322/ENST00000378322.gff ... Indexed 1 transcripts, 11 exons, 11 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000368801/ENST00000368801.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000368801/ENST00000368801.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000368801/compound-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000368801/ENST00000368801.gff ... Indexed 1 transcripts, 3 exons, 2 CDSs, 3 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000227471/ENST00000227471.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000227471/ENST00000227471.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000227471/ENST00000227471.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000520868/ENST00000520868.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000520868/ENST00000520868.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000520868/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000520868/ENST00000520868.gff ... Indexed 1 transcripts, 6 exons, 5 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000448695/ENST00000448695.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000448695/ENST00000448695.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000448695/ENST00000448695.gff ... Indexed 1 transcripts, 26 exons, 26 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000413103/ENST00000413103.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000413103/ENST00000413103.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000413103/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000413103/ENST00000413103.gff ... Indexed 1 transcripts, 2 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000436063/ENST00000436063.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000436063/ENST00000436063.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000436063/insert-before-utr.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000436063/ENST00000436063.gff ... Indexed 1 transcripts, 7 exons, 7 CDSs, 2 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000294661/ENST00000294661.gff ... Indexed 1 transcripts, 4 exons, 0 CDSs, 0 UTRs Calling... .. ok Number of tests: total .. 801 passed .. 801 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: bcftools-1.9-1.fc31.ppc64le Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.iDSfrh + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.9 + DOCDIR=/builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/share/doc/bcftools + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/share/doc/bcftools + cp -pr AUTHORS /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/share/doc/bcftools + cp -pr NEWS /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/share/doc/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.K4dH5k + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.9 + LICENSEDIR=/builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/share/licenses/bcftools + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/share/licenses/bcftools + cp -pr LICENSE /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le/usr/share/licenses/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Provides: bcftools = 1.9-1.fc31 bcftools(ppc-64) = 1.9-1.fc31 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()(64bit) libc.so.6(GLIBC_2.17)(64bit) libdl.so.2()(64bit) libdl.so.2(GLIBC_2.17)(64bit) libgsl.so.23()(64bit) libgslcblas.so.0()(64bit) libhts.so.2()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libperl.so.5.30()(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.17)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Conflicts: samtools < 1.0 Processing files: bcftools-debugsource-1.9-1.fc31.ppc64le Provides: bcftools-debugsource = 1.9-1.fc31 bcftools-debugsource(ppc-64) = 1.9-1.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bcftools-debuginfo-1.9-1.fc31.ppc64le Provides: bcftools-debuginfo = 1.9-1.fc31 bcftools-debuginfo(ppc-64) = 1.9-1.fc31 debuginfo(build-id) = 23dda915655efd8e942ff1a51fdf03f65993b6d0 debuginfo(build-id) = 2954f4f6d574439f0e9d4228835658655d0c3e4f debuginfo(build-id) = 3c9a4a5772341bf7231ea2d1bd18639966749bdc debuginfo(build-id) = 4387d964814d9467ac1b4aed702094ec0c5cf5cd debuginfo(build-id) = 460742e6a13c214ce2c899d84adba84021d1ef3c debuginfo(build-id) = 47881ff63bdf676dae5a5086d164d8441e96ab07 debuginfo(build-id) = 4f0d7a808dcc0597896b6ab890d707a585acc68c debuginfo(build-id) = 5927d74a0dc97df812ac31a4b0e00750b38e769b debuginfo(build-id) = 60485d2e89113eae808211e791a700ee7eefac3d debuginfo(build-id) = 81d32ee21d4067074fcafeb2e6b2addaa7d0db13 debuginfo(build-id) = 8435997f5684b07d0de0b7233c4312ec54b87951 debuginfo(build-id) = 87e0dee3bb49984e53bacca0d91238f7144699c7 debuginfo(build-id) = 95c97ff18377e7260f3fa86fc7aa0bb34d0874fe debuginfo(build-id) = a2990e22489bef9a0c25286ad4c23da590ceef6d debuginfo(build-id) = a6a5ea2d7980f4611c69afbabcffd826763a0a43 debuginfo(build-id) = aa9df4390954483af2d325ce1770f6841b041809 debuginfo(build-id) = abb69ead6cfafa3830cd019e93c800823685f4f1 debuginfo(build-id) = b3d22425ce3c81f37f65d28df1e8fc2c8bbf2ced debuginfo(build-id) = b668cd1b200c2422f00be83d3d5d6e67b95d5c03 debuginfo(build-id) = bfb9e6fe009b129167944f60cd96c263f51883ee debuginfo(build-id) = d54534f9eaf3f6e7997c2d2b8707ec8fab358749 debuginfo(build-id) = d54b7974a5ceaeda0e73354c18bcdd3259440eb9 debuginfo(build-id) = dd5912cf582703e7e323ce37b437b9931de09712 debuginfo(build-id) = e2ce3307907addbee60d82cdd8fe4521ea069f57 debuginfo(build-id) = e718d85b8d5f19d61c16f66c9e4b77e726721bec debuginfo(build-id) = e8fd58e92a2a3e79e8972d3184504e998656c48c debuginfo(build-id) = f148221454c1fc701230dace98d4cdceb187b15a debuginfo(build-id) = fba486299fb519e537cc0e1ac0758937e80fa04c debuginfo(build-id) = fe76f68745829401e98fde43be5952d3426ff507 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bcftools-debugsource(ppc-64) = 1.9-1.fc31 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le Wrote: /builddir/build/RPMS/bcftools-1.9-1.fc31.ppc64le.rpm Wrote: /builddir/build/RPMS/bcftools-debugsource-1.9-1.fc31.ppc64le.rpm Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.9-1.fc31.ppc64le.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.ecU7ah + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.9 + /usr/bin/rm -rf /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.ppc64le + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0