Mock Version: 1.4.21 Mock Version: 1.4.21 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/bcftools.spec'], chrootPath='/var/lib/mock/f31-build-18404079-1310166/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 x86_64 --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: x86_64 Building for target x86_64 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 x86_64 --nodeps /builddir/build/SPECS/bcftools.spec'], chrootPath='/var/lib/mock/f31-build-18404079-1310166/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 x86_64 --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: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1574121600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.PGmQvx + 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.Hh9Duw + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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=x86_64-redhat-linux-gnu --host=x86_64-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' --prefix=/usr --with-htslib=system --enable-perl-filters --enable-libgsl '--with-bcf-plugin-path=/usr/local/libexec/bcftools:$(plugindir)' checking for x86_64-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 -j6 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -DPLUGINPATH='"/usr/local/libexec/bcftools:/usr/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o peakfit.o peakfit.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -c -o bam_sample.o bam_sample.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/tag2tag.so version.c plugins/tag2tag.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/dosage.so version.c plugins/dosage.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/GTisec.so version.c plugins/GTisec.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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl 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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -DUSE_GPL -c -o main.o main.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/GTsubset.so version.c plugins/GTsubset.c -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/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.UPbBjt + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64 ++ dirname /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64 + cd bcftools-1.9 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/bin /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/share/man/man1 /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools /usr/bin/install -p bcftools /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/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.x86_64/usr/bin /usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/share/man/man1 /usr/bin/install -p plugins/*.so /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools + /usr/lib/rpm/find-debuginfo.sh -j6 --strict-build-id -m -i --build-id-seed 1.9-1.fc31 --unique-debug-suffix -1.9-1.fc31.x86_64 --unique-debug-src-base bcftools-1.9-1.fc31.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -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.x86_64/usr/bin/bcftools explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/ad-bias.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/GTsubset.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/af-dist.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/GTisec.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/check-ploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/bin/bcftools extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/ad-bias.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/GTisec.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/GTsubset.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/af-dist.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/check-ploidy.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/check-sparsity.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/color-chrs.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/check-sparsity.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/color-chrs.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/contrast.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/contrast.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/counts.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/counts.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/dosage.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/dosage.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/fill-AN-AC.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/fill-AN-AC.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/fill-from-fasta.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/fill-from-fasta.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/fixploidy.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/fill-tags.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/fixref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/fixploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/fixref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/fill-tags.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/frameshifts.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/frameshifts.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/guess-ploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/guess-ploidy.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/impute-info.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/impute-info.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/isecGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/isecGT.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/mendelian.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/missing2ref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/mendelian.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/missing2ref.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/prune.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/prune.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/setGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/setGT.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/split.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/smpl-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/split.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/smpl-stats.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/trio-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/trio-stats.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/tag2tag.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/tag2tag.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/trio-switch-rate.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/libexec/bcftools/trio-switch-rate.so original debug info size: 6384kB, size after compression: 5924kB /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.XESCSt + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.9 + ldd bcftools + grep -E '/lib(64)?/libhts\.so\.' libhts.so.2 => /lib64/libhts.so.2 (0x00007fefbf3dc000) + 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/test.pl: module IO::Pty not found; skipping usage tests test_usage: bcftools test_tabix: tabix /tmp/FoFC1ZbqFY/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/FoFC1ZbqFY/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/FoFC1ZbqFY/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/FoFC1ZbqFY/merge.a.bcf 1:3000151-3000151 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/FoFC1ZbqFY/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/FoFC1ZbqFY/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/FoFC1ZbqFY/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/FoFC1ZbqFY/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/FoFC1ZbqFY/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/FoFC1ZbqFY/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/FoFC1ZbqFY/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/FoFC1ZbqFY/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/FoFC1ZbqFY/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/FoFC1ZbqFY/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/FoFC1ZbqFY/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/FoFC1ZbqFY/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/FoFC1ZbqFY/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/FoFC1ZbqFY/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/FoFC1ZbqFY/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/FoFC1ZbqFY/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/FoFC1ZbqFY/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/FoFC1ZbqFY/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/FoFC1ZbqFY/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/FoFC1ZbqFY/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/FoFC1ZbqFY/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/FoFC1ZbqFY/empty.bcf .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.9/bcftools stats -s - /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/check.1.chk /tmp/FoFC1ZbqFY/check.2.chk /tmp/FoFC1ZbqFY/check.3.chk /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/stats.a.vcf.gz /tmp/FoFC1ZbqFY/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.9/bcftools stats -s B /tmp/FoFC1ZbqFY/stats.a.vcf.gz /tmp/FoFC1ZbqFY/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.9/bcftools stats -s - /tmp/FoFC1ZbqFY/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -n =2 /tmp/FoFC1ZbqFY/isec.a.vcf.gz /tmp/FoFC1ZbqFY/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -Ob -n =2 /tmp/FoFC1ZbqFY/isec.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/isec.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/isec.a.vcf.gz /tmp/FoFC1ZbqFY/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -n =2 -c both /tmp/FoFC1ZbqFY/isec.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/isec.a.vcf.gz /tmp/FoFC1ZbqFY/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -n =2 -c any /tmp/FoFC1ZbqFY/isec.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/isec.a.vcf.gz /tmp/FoFC1ZbqFY/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -C -c any /tmp/FoFC1ZbqFY/isec.a.vcf.gz /tmp/FoFC1ZbqFY/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -Ob -C -c any /tmp/FoFC1ZbqFY/isec.a.vcf.gz /tmp/FoFC1ZbqFY/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.9/bcftools isec --no-version -T /tmp/FoFC1ZbqFY/isec.tab.gz /tmp/FoFC1ZbqFY/isec.a.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.9/bcftools isec -Ob -T /tmp/FoFC1ZbqFY/isec.tab.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/merge.a.vcf.gz /tmp/FoFC1ZbqFY/merge.b.vcf.gz /tmp/FoFC1ZbqFY/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples /tmp/FoFC1ZbqFY/merge.a.vcf.gz /tmp/FoFC1ZbqFY/merge.b.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/merge.a.vcf.gz /tmp/FoFC1ZbqFY/merge.b.vcf.gz /tmp/FoFC1ZbqFY/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -Fx /tmp/FoFC1ZbqFY/merge.a.vcf.gz /tmp/FoFC1ZbqFY/merge.b.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/merge.a.vcf.gz /tmp/FoFC1ZbqFY/merge.b.vcf.gz /tmp/FoFC1ZbqFY/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -0 /tmp/FoFC1ZbqFY/merge.a.vcf.gz /tmp/FoFC1ZbqFY/merge.b.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/merge.2.a.vcf.gz /tmp/FoFC1ZbqFY/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -m none /tmp/FoFC1ZbqFY/merge.2.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/merge.2.a.vcf.gz /tmp/FoFC1ZbqFY/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -m both /tmp/FoFC1ZbqFY/merge.2.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/merge.2.a.vcf.gz /tmp/FoFC1ZbqFY/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -m all /tmp/FoFC1ZbqFY/merge.2.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/merge.3.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/merge.3.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/merge.4.a.vcf.gz /tmp/FoFC1ZbqFY/merge.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -m id /tmp/FoFC1ZbqFY/merge.4.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/gvcf.merge.1.vcf.gz /tmp/FoFC1ZbqFY/gvcf.merge.2.vcf.gz /tmp/FoFC1ZbqFY/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/FoFC1ZbqFY/gvcf.merge.1.vcf.gz /tmp/FoFC1ZbqFY/gvcf.merge.2.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/merge.gvcf.2.a.vcf.gz /tmp/FoFC1ZbqFY/merge.gvcf.2.b.vcf.gz /tmp/FoFC1ZbqFY/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/FoFC1ZbqFY/merge.gvcf.2.a.vcf.gz /tmp/FoFC1ZbqFY/merge.gvcf.2.b.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/merge.gvcf.3.a.vcf.gz /tmp/FoFC1ZbqFY/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --gvcf - -i SRC:join /tmp/FoFC1ZbqFY/merge.gvcf.3.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/merge.5.a.vcf.gz /tmp/FoFC1ZbqFY/merge.5.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob /tmp/FoFC1ZbqFY/merge.5.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vectors.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter.4.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m- /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m- /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m+ /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m+ /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/norm.merge.3.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m+ /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m+ -s /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d snps /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d indels /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d both /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d all /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d none /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vcf.gz -r20,Y .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -f PASS -Xks NA00003 /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -xs NA00003 /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -p /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -P /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -GVsnps /tmp/FoFC1ZbqFY/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -GVsnps /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -s ^NA00003 /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -G /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -a /tmp/FoFC1ZbqFY/many.alleles.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -a /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -asA /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -asB /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.vectors.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -asA /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -i'TXT0="text"' /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -i 'POS>=3062917' /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -c6:nonmajor /tmp/FoFC1ZbqFY/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -q0.3:major /tmp/FoFC1ZbqFY/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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.5Uzg5N 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.5IAPd3 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.MQ95om 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.CER8Wx 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/FoFC1ZbqFY/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/FoFC1ZbqFY/regions.tab.gz /tmp/FoFC1ZbqFY/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/FoFC1ZbqFY/regions.tab.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/FoFC1ZbqFY/regions.tab.gz /tmp/FoFC1ZbqFY/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/FoFC1ZbqFY/regions.bed /tmp/FoFC1ZbqFY/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/FoFC1ZbqFY/regions.bed .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/FoFC1ZbqFY/regions.bed /tmp/FoFC1ZbqFY/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/FoFC1ZbqFY/regions.bed.gz /tmp/FoFC1ZbqFY/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/FoFC1ZbqFY/regions.bed.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/FoFC1ZbqFY/regions.bed.gz /tmp/FoFC1ZbqFY/regions.vcf.gz .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots4.vcf.gz -c +INFO /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots4.vcf.gz -c +INFO /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots11.vcf.gz -c FMT /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/annots11.vcf.gz -c FMT /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +missing2ref --no-version /tmp/FoFC1ZbqFY/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +setGT --no-version /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +dosage /tmp/FoFC1ZbqFY/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +dosage /tmp/FoFC1ZbqFY/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fixploidy --no-version /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa -i /tmp/FoFC1ZbqFY/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fixref /tmp/FoFC1ZbqFY/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa -i /tmp/FoFC1ZbqFY/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fixref /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/concat.1.a.vcf.gz /tmp/FoFC1ZbqFY/concat.1.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob /tmp/FoFC1ZbqFY/concat.1.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/concat.1.a.bcf /tmp/FoFC1ZbqFY/concat.1.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob /tmp/FoFC1ZbqFY/concat.1.a.bcf /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/concat.2.a.vcf.gz /tmp/FoFC1ZbqFY/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -a /tmp/FoFC1ZbqFY/concat.2.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/concat.2.a.bcf /tmp/FoFC1ZbqFY/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -a /tmp/FoFC1ZbqFY/concat.2.a.bcf /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/concat.2.a.vcf.gz /tmp/FoFC1ZbqFY/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -aD /tmp/FoFC1ZbqFY/concat.2.a.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/concat.2.a.bcf /tmp/FoFC1ZbqFY/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -aD /tmp/FoFC1ZbqFY/concat.2.a.bcf /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/concat.3.a.vcf.gz /tmp/FoFC1ZbqFY/concat.3.b.vcf.gz /tmp/FoFC1ZbqFY/concat.3.0.vcf.gz /tmp/FoFC1ZbqFY/concat.3.c.vcf.gz /tmp/FoFC1ZbqFY/concat.3.d.vcf.gz /tmp/FoFC1ZbqFY/concat.3.e.vcf.gz /tmp/FoFC1ZbqFY/concat.3.f.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -l /tmp/FoFC1ZbqFY/concat.3.a.vcf.gz /tmp/FoFC1ZbqFY/concat.3.b.vcf.gz /tmp/FoFC1ZbqFY/concat.3.0.vcf.gz /tmp/FoFC1ZbqFY/concat.3.c.vcf.gz /tmp/FoFC1ZbqFY/concat.3.d.vcf.gz /tmp/FoFC1ZbqFY/concat.3.e.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/concat.3.a.bcf /tmp/FoFC1ZbqFY/concat.3.b.bcf /tmp/FoFC1ZbqFY/concat.3.0.bcf /tmp/FoFC1ZbqFY/concat.3.c.bcf /tmp/FoFC1ZbqFY/concat.3.d.bcf /tmp/FoFC1ZbqFY/concat.3.e.bcf /tmp/FoFC1ZbqFY/concat.3.f.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -l /tmp/FoFC1ZbqFY/concat.3.a.bcf /tmp/FoFC1ZbqFY/concat.3.b.bcf /tmp/FoFC1ZbqFY/concat.3.0.bcf /tmp/FoFC1ZbqFY/concat.3.c.bcf /tmp/FoFC1ZbqFY/concat.3.d.bcf /tmp/FoFC1ZbqFY/concat.3.e.bcf /tmp/FoFC1ZbqFY/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 2634516635 .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat --naive /tmp/FoFC1ZbqFY/naive_concat.0.bcf /tmp/FoFC1ZbqFY/naive_concat.1.bcf /tmp/FoFC1ZbqFY/naive_concat.2.bcf /tmp/FoFC1ZbqFY/naive_concat.3.bcf /tmp/FoFC1ZbqFY/naive_concat.4.bcf /tmp/FoFC1ZbqFY/naive_concat.5.bcf /tmp/FoFC1ZbqFY/naive_concat.6.bcf /tmp/FoFC1ZbqFY/naive_concat.7.bcf /tmp/FoFC1ZbqFY/naive_concat.8.bcf /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/naive_concat.0.vcf.gz /tmp/FoFC1ZbqFY/naive_concat.1.vcf.gz /tmp/FoFC1ZbqFY/naive_concat.2.vcf.gz /tmp/FoFC1ZbqFY/naive_concat.3.vcf.gz /tmp/FoFC1ZbqFY/naive_concat.4.vcf.gz /tmp/FoFC1ZbqFY/naive_concat.5.vcf.gz /tmp/FoFC1ZbqFY/naive_concat.6.vcf.gz /tmp/FoFC1ZbqFY/naive_concat.7.vcf.gz /tmp/FoFC1ZbqFY/naive_concat.8.vcf.gz /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/empty.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/rename.map -Ov /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/rename.map -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/convert.hap-missing.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/convert.gvcf.vcf.gz 2>/dev/null .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/FoFC1ZbqFY/consensus.1.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/FoFC1ZbqFY/consensus.2.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/FoFC1ZbqFY/consensus.3.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus.fa -H 1 -c /tmp/FoFC1ZbqFY/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/FoFC1ZbqFY/consensus.4.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/FoFC1ZbqFY/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/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/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/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/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-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/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/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/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/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/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-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-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/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/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/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/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/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/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/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/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/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/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/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/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/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 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 Number of tests: total .. 801 passed .. 801 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: bcftools-1.9-1.fc31.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.l50wxu + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.9 + DOCDIR=/builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/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.x86_64/usr/share/doc/bcftools + cp -pr AUTHORS /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/share/doc/bcftools + cp -pr NEWS /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/share/doc/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.gjpeAt + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.9 + LICENSEDIR=/builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/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.x86_64/usr/share/licenses/bcftools + cp -pr LICENSE /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64/usr/share/licenses/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Provides: bcftools = 1.9-1.fc31 bcftools(x86-64) = 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_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libdl.so.2()(64bit) libdl.so.2(GLIBC_2.2.5)(64bit) libgsl.so.23()(64bit) libgslcblas.so.0()(64bit) libhts.so.2()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(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_2.2.5)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Conflicts: samtools < 1.0 Processing files: bcftools-debugsource-1.9-1.fc31.x86_64 Provides: bcftools-debugsource = 1.9-1.fc31 bcftools-debugsource(x86-64) = 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.x86_64 Provides: bcftools-debuginfo = 1.9-1.fc31 bcftools-debuginfo(x86-64) = 1.9-1.fc31 debuginfo(build-id) = 122b733518ba4d01f888fed306beeaa52e517694 debuginfo(build-id) = 1877b58c45b5727bab2326dba5f7886da0af86ed debuginfo(build-id) = 1e94ac016acb5f9c325001abb61265a3249a4509 debuginfo(build-id) = 2dc26bc823a3451d64810e27451aed26466dcf42 debuginfo(build-id) = 2f3fca73727b8fce9883d6f9b7c37178850266c8 debuginfo(build-id) = 3974a2db5e34ac286c5863a735be0f634e649769 debuginfo(build-id) = 3b0b03433a3485bea97c7c79c78f4412acfb9044 debuginfo(build-id) = 3d6d6d255274ac885d44efd489da22a4e4558d6b debuginfo(build-id) = 6a8c092c31d987edf09174b268b817d87e7324cc debuginfo(build-id) = 6cfebae3273fd1a0355891cb9e00992f75de112f debuginfo(build-id) = 729b39861aa33b4bb944d85fa133b56aded20ffe debuginfo(build-id) = 7f708d455de41783b3f8c1490221dff0c4708897 debuginfo(build-id) = 88cc50b1c978021759e6132d31311549eee567af debuginfo(build-id) = 9649ecf0a4a62f326fa2662d2f308bad11402ad5 debuginfo(build-id) = 9a0757c876d619c69cc27606504390ff9bfe8dca debuginfo(build-id) = 9f1fd9f88393bf10b7ee86864ae1c0dc32a36c4a debuginfo(build-id) = a535860a8e215be9bb1fd71e67935b8d35fd5396 debuginfo(build-id) = b31e525b7fcc2f93043413a4b65f1e9e6afce59d debuginfo(build-id) = b56ec02ec762ec2c7a5960c27224999a8791fc99 debuginfo(build-id) = b839d16ea8434e109c60a798b9fcc7eeec4e8547 debuginfo(build-id) = c4c92a16b03cd1c383b6c5934b6af7a2df476200 debuginfo(build-id) = cc6971523709466263249013a878f367543a73e9 debuginfo(build-id) = d6783e52d7b2567a89edbe3d22643041414327eb debuginfo(build-id) = db8396786be4e0651c08287cf950c19a729c6411 debuginfo(build-id) = deb56b3a6a8bffc758b966a7ae53ee8a1d05d7a8 debuginfo(build-id) = edf8fd61e659fd72489e50bcedeaa956c5cb26e5 debuginfo(build-id) = f03895e93fc561dffa119349b214e67d55e1ad0a debuginfo(build-id) = f1d47e3fab9c223b952d5fa9574011489b35d54d debuginfo(build-id) = f7075d2c25b818fcfa5ea81814168fe6a82c4c9c Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bcftools-debugsource(x86-64) = 1.9-1.fc31 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64 Wrote: /builddir/build/RPMS/bcftools-1.9-1.fc31.x86_64.rpm Wrote: /builddir/build/RPMS/bcftools-debugsource-1.9-1.fc31.x86_64.rpm Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.9-1.fc31.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.d74qEw + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.9 + /usr/bin/rm -rf /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0