Mock Version: 1.4.21 Mock Version: 1.4.21 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/bcftools.spec'], chrootPath='/var/lib/mock/f31-build-18404081-1310166/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 armv7hl --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: armv7hl Building for target armv7hl 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 armv7hl --nodeps /builddir/build/SPECS/bcftools.spec'], chrootPath='/var/lib/mock/f31-build-18404081-1310166/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 armv7hl --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: armv7hl Building for target armv7hl setting SOURCE_DATE_EPOCH=1574121600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.bBMILE + 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 . + echo 'Patch #0 (bcftools-1.9-python3.patch):' 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.cGQ09D + 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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard' + 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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard' + 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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -I/usr/lib/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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -I/usr/lib/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=armv7hl-redhat-linux-gnu --host=armv7hl-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard' '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 armv7hl-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... 64 checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -ldl checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for gsl/gsl_version.h... yes checking for library containing cblas_dgemm... -lgslcblas checking for gsl_multifit_gradient in -lgsl... yes configure: creating ./config.status config.status: creating config.mk config.status: creating config.h configure: License has been changed to GPL. Linking against the GNU scientific library requires that the resulting binary is licensed using the GNU General Public License. In particular, this means you will have to follow the terms of this license in order to distribute binary copies. For more information see the INSTALL file. Text of the GNU General Public License can be found in the LICENSE file, or at http://www.gnu.org/copyleft/gpl.html Information on the GNU Scientific Library, including the rationale for its choice of license can be found at https://www.gnu.org/software/gsl/ + /usr/bin/make -O -j4 V=1 VERBOSE=1 echo '#define BCFTOOLS_VERSION "1.9"' > version.h gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -I. -c -o vcfmerge.o vcfmerge.c vcfmerge.c: In function 'maux_init': vcfmerge.c:682:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/perl5/CORE -c -o filter.o filter.c gcc -O2 -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -I. -c -o bam_sample.o bam_sample.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -I. -c -o test/test-regidx.o test/test-regidx.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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -I. -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl gcc -fPIC -shared -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -I. -DUSE_GPL -c -o main.o main.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o test/test-rbuf test/test-rbuf.o -lz -ldl -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 -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -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/lib/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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/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.DGWLwE + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm ++ dirname /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm + cd bcftools-1.9 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/bin /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/share/man/man1 /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools /usr/bin/install -p bcftools /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/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.arm/usr/bin /usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/share/man/man1 /usr/bin/install -p plugins/*.so /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools + /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.9-1.fc31 --unique-debug-suffix -1.9-1.fc31.arm --unique-debug-src-base bcftools-1.9-1.fc31.arm --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bcftools-1.9 explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/ad-bias.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/GTsubset.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/bin/bcftools explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/GTisec.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/GTsubset.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/ad-bias.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/GTisec.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/bin/bcftools explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/af-dist.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/check-ploidy.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/check-sparsity.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/af-dist.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/check-ploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/check-sparsity.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/contrast.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/color-chrs.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/counts.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/dosage.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/contrast.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/color-chrs.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/dosage.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/counts.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/fill-AN-AC.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/fill-from-fasta.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/fill-tags.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/fill-AN-AC.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/fill-from-fasta.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/fixploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/fill-tags.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/fixploidy.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/fixref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/fixref.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/frameshifts.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/guess-ploidy.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/frameshifts.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/guess-ploidy.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/impute-info.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/impute-info.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/isecGT.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/mendelian.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/missing2ref.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/isecGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/mendelian.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/missing2ref.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/prune.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/prune.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/setGT.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/setGT.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/smpl-stats.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/split.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/split.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/smpl-stats.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/tag2tag.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/tag2tag.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/trio-stats.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/trio-switch-rate.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/trio-stats.so extracting debug info from /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/libexec/bcftools/trio-switch-rate.so original debug info size: 5084kB, size after compression: 4652kB /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.NA5ACE + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.9 + ldd bcftools + grep -E '/lib(64)?/libhts\.so\.' libhts.so.2 => /lib/libhts.so.2 (0xb6d9c000) + 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/2uenORsFxA/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/2uenORsFxA/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/2uenORsFxA/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/2uenORsFxA/merge.a.bcf 1:3000151-3000151 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/2uenORsFxA/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/2uenORsFxA/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/2uenORsFxA/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/2uenORsFxA/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/2uenORsFxA/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/2uenORsFxA/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/2uenORsFxA/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/2uenORsFxA/large_chrom_csi_limit.bcf chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/2uenORsFxA/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /builddir/build/BUILD/bcftools-1.9/bcftools view -H /tmp/2uenORsFxA/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/2uenORsFxA/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/2uenORsFxA/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/2uenORsFxA/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/2uenORsFxA/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/2uenORsFxA/idx.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/2uenORsFxA/idx.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/2uenORsFxA/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/2uenORsFxA/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -s /tmp/2uenORsFxA/empty.bcf .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/2uenORsFxA/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/2uenORsFxA/empty.vcf.gz .. ok test_vcf_idxstats: /builddir/build/BUILD/bcftools-1.9/bcftools index -n /tmp/2uenORsFxA/empty.bcf .. ok test_vcf_check: /builddir/build/BUILD/bcftools-1.9/bcftools stats -s - /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/check.1.chk /tmp/2uenORsFxA/check.2.chk /tmp/2uenORsFxA/check.3.chk /tmp/2uenORsFxA/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/2uenORsFxA/stats.a.vcf.gz /tmp/2uenORsFxA/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.9/bcftools stats -s B /tmp/2uenORsFxA/stats.a.vcf.gz /tmp/2uenORsFxA/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /builddir/build/BUILD/bcftools-1.9/bcftools stats -s - /tmp/2uenORsFxA/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -n =2 /tmp/2uenORsFxA/isec.a.vcf.gz /tmp/2uenORsFxA/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -Ob -n =2 /tmp/2uenORsFxA/isec.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/isec.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/isec.a.vcf.gz /tmp/2uenORsFxA/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -n =2 -c both /tmp/2uenORsFxA/isec.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/isec.a.vcf.gz /tmp/2uenORsFxA/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -n =2 -c any /tmp/2uenORsFxA/isec.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/isec.a.vcf.gz /tmp/2uenORsFxA/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -C -c any /tmp/2uenORsFxA/isec.a.vcf.gz /tmp/2uenORsFxA/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec: /builddir/build/BUILD/bcftools-1.9/bcftools isec -Ob -C -c any /tmp/2uenORsFxA/isec.a.vcf.gz /tmp/2uenORsFxA/isec.b.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.9/bcftools isec --no-version -T /tmp/2uenORsFxA/isec.tab.gz /tmp/2uenORsFxA/isec.a.vcf.gz 2>/dev/null .. ok test_vcf_isec2: /builddir/build/BUILD/bcftools-1.9/bcftools isec -Ob -T /tmp/2uenORsFxA/isec.tab.gz /tmp/2uenORsFxA/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/2uenORsFxA/merge.a.vcf.gz /tmp/2uenORsFxA/merge.b.vcf.gz /tmp/2uenORsFxA/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples /tmp/2uenORsFxA/merge.a.vcf.gz /tmp/2uenORsFxA/merge.b.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/merge.a.vcf.gz /tmp/2uenORsFxA/merge.b.vcf.gz /tmp/2uenORsFxA/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -Fx /tmp/2uenORsFxA/merge.a.vcf.gz /tmp/2uenORsFxA/merge.b.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/merge.a.vcf.gz /tmp/2uenORsFxA/merge.b.vcf.gz /tmp/2uenORsFxA/merge.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -0 /tmp/2uenORsFxA/merge.a.vcf.gz /tmp/2uenORsFxA/merge.b.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/merge.2.a.vcf.gz /tmp/2uenORsFxA/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -m none /tmp/2uenORsFxA/merge.2.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/merge.2.a.vcf.gz /tmp/2uenORsFxA/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -m both /tmp/2uenORsFxA/merge.2.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/merge.2.a.vcf.gz /tmp/2uenORsFxA/merge.2.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -m all /tmp/2uenORsFxA/merge.2.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/merge.3.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/merge.3.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/merge.4.a.vcf.gz /tmp/2uenORsFxA/merge.4.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --force-samples -m id /tmp/2uenORsFxA/merge.4.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/gvcf.merge.1.vcf.gz /tmp/2uenORsFxA/gvcf.merge.2.vcf.gz /tmp/2uenORsFxA/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/2uenORsFxA/gvcf.merge.1.vcf.gz /tmp/2uenORsFxA/gvcf.merge.2.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/merge.gvcf.2.a.vcf.gz /tmp/2uenORsFxA/merge.gvcf.2.b.vcf.gz /tmp/2uenORsFxA/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --gvcf - /tmp/2uenORsFxA/merge.gvcf.2.a.vcf.gz /tmp/2uenORsFxA/merge.gvcf.2.b.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/merge.gvcf.3.a.vcf.gz /tmp/2uenORsFxA/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob --gvcf - -i SRC:join /tmp/2uenORsFxA/merge.gvcf.3.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/merge.5.a.vcf.gz /tmp/2uenORsFxA/merge.5.b.vcf.gz .. ok test_vcf_merge: /builddir/build/BUILD/bcftools-1.9/bcftools merge -Ob /tmp/2uenORsFxA/merge.5.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.vectors.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter-type.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/filter-missing-floats.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/missing.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter.2.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter.3.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter.4.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/query.filter.5.vcf.gz .. ok test_vcf_query: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/norm.split.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m- /tmp/2uenORsFxA/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/2uenORsFxA/norm.split.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m- /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m+ /tmp/2uenORsFxA/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/2uenORsFxA/norm.merge.2.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m+ /tmp/2uenORsFxA/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/2uenORsFxA/norm.merge.3.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m+ /tmp/2uenORsFxA/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/2uenORsFxA/norm.merge.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -m+ -s /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d snps /tmp/2uenORsFxA/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/2uenORsFxA/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d indels /tmp/2uenORsFxA/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/2uenORsFxA/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d both /tmp/2uenORsFxA/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/2uenORsFxA/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d all /tmp/2uenORsFxA/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/2uenORsFxA/norm.rmdup.vcf.gz 2>/dev/null .. ok test_vcf_norm: /builddir/build/BUILD/bcftools-1.9/bcftools norm -Ob -d none /tmp/2uenORsFxA/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/2uenORsFxA/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/2uenORsFxA/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/2uenORsFxA/view.vcf.gz -r20,Y .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -f PASS -Xks NA00003 /tmp/2uenORsFxA/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/2uenORsFxA/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -xs NA00003 /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -p /tmp/2uenORsFxA/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/2uenORsFxA/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -P /tmp/2uenORsFxA/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/2uenORsFxA/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/2uenORsFxA/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/2uenORsFxA/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -GVsnps /tmp/2uenORsFxA/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -GVsnps /tmp/2uenORsFxA/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/2uenORsFxA/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/2uenORsFxA/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/2uenORsFxA/view.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -s ^NA00003 /tmp/2uenORsFxA/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/2uenORsFxA/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -G /tmp/2uenORsFxA/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/2uenORsFxA/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -a /tmp/2uenORsFxA/many.alleles.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -a /tmp/2uenORsFxA/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/2uenORsFxA/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -asA /tmp/2uenORsFxA/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/2uenORsFxA/view.vectors.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -asB /tmp/2uenORsFxA/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/2uenORsFxA/view.vectors.2.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -asA /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/view.filter.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -i'TXT0="text"' /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob -i 'POS>=3062917' /tmp/2uenORsFxA/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/2uenORsFxA/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -c6:nonmajor /tmp/2uenORsFxA/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -q0.3:major /tmp/2uenORsFxA/view.minmaxac.vcf.gz .. ok test_vcf_view: /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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.AoN6Bu 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.csYyhF 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.aXG0bY Merging 3 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.wEQOxe Merging 3 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/2uenORsFxA/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/2uenORsFxA/regions.tab.gz /tmp/2uenORsFxA/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/2uenORsFxA/regions.tab.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/2uenORsFxA/regions.tab.gz /tmp/2uenORsFxA/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/2uenORsFxA/regions.bed /tmp/2uenORsFxA/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/2uenORsFxA/regions.bed .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/2uenORsFxA/regions.bed /tmp/2uenORsFxA/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/2uenORsFxA/regions.bed.gz /tmp/2uenORsFxA/regions.vcf.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/2uenORsFxA/regions.bed.gz .. ok test_vcf_regions: /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/2uenORsFxA/regions.bed.gz /tmp/2uenORsFxA/regions.vcf.gz .. ok test_vcf_annotate: /builddir/build/BUILD/bcftools-1.9/bcftools annotate -a /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/2uenORsFxA/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/2uenORsFxA/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/2uenORsFxA/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/2uenORsFxA/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/2uenORsFxA/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/2uenORsFxA/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/2uenORsFxA/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/2uenORsFxA/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/2uenORsFxA/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/2uenORsFxA/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/2uenORsFxA/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/2uenORsFxA/annots4.vcf.gz -c +INFO /tmp/2uenORsFxA/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/2uenORsFxA/annots4.vcf.gz -c +INFO /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/2uenORsFxA/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/2uenORsFxA/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/2uenORsFxA/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/2uenORsFxA/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/2uenORsFxA/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/2uenORsFxA/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/2uenORsFxA/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/2uenORsFxA/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/2uenORsFxA/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/2uenORsFxA/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/2uenORsFxA/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/2uenORsFxA/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/2uenORsFxA/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/2uenORsFxA/annots11.vcf.gz -c FMT /tmp/2uenORsFxA/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/2uenORsFxA/annots11.vcf.gz -c FMT /tmp/2uenORsFxA/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/2uenORsFxA/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +missing2ref --no-version /tmp/2uenORsFxA/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +setGT --no-version /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +dosage /tmp/2uenORsFxA/plugin1.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +dosage /tmp/2uenORsFxA/plugin1.bcf 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fixploidy --no-version /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/fill-tags-hemi.bcf -- -d 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/2uenORsFxA/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/2uenORsFxA/view.bcf | grep -v bcftools 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +GTisec /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa -i /tmp/2uenORsFxA/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fixref /tmp/2uenORsFxA/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.9/test/norm.fa -i /tmp/2uenORsFxA/fixref.2b.vcf.gz 2>/dev/null | grep -v ^##bcftools_ .. ok test_vcf_plugin: /builddir/build/BUILD/bcftools-1.9/bcftools +fixref /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/concat.1.a.vcf.gz /tmp/2uenORsFxA/concat.1.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob /tmp/2uenORsFxA/concat.1.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/concat.1.a.bcf /tmp/2uenORsFxA/concat.1.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob /tmp/2uenORsFxA/concat.1.a.bcf /tmp/2uenORsFxA/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/2uenORsFxA/concat.2.a.vcf.gz /tmp/2uenORsFxA/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -a /tmp/2uenORsFxA/concat.2.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/concat.2.a.bcf /tmp/2uenORsFxA/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -a /tmp/2uenORsFxA/concat.2.a.bcf /tmp/2uenORsFxA/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/2uenORsFxA/concat.2.a.vcf.gz /tmp/2uenORsFxA/concat.2.b.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -aD /tmp/2uenORsFxA/concat.2.a.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/concat.2.a.bcf /tmp/2uenORsFxA/concat.2.b.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -aD /tmp/2uenORsFxA/concat.2.a.bcf /tmp/2uenORsFxA/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/2uenORsFxA/concat.3.a.vcf.gz /tmp/2uenORsFxA/concat.3.b.vcf.gz /tmp/2uenORsFxA/concat.3.0.vcf.gz /tmp/2uenORsFxA/concat.3.c.vcf.gz /tmp/2uenORsFxA/concat.3.d.vcf.gz /tmp/2uenORsFxA/concat.3.e.vcf.gz /tmp/2uenORsFxA/concat.3.f.vcf.gz .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -l /tmp/2uenORsFxA/concat.3.a.vcf.gz /tmp/2uenORsFxA/concat.3.b.vcf.gz /tmp/2uenORsFxA/concat.3.0.vcf.gz /tmp/2uenORsFxA/concat.3.c.vcf.gz /tmp/2uenORsFxA/concat.3.d.vcf.gz /tmp/2uenORsFxA/concat.3.e.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/concat.3.a.bcf /tmp/2uenORsFxA/concat.3.b.bcf /tmp/2uenORsFxA/concat.3.0.bcf /tmp/2uenORsFxA/concat.3.c.bcf /tmp/2uenORsFxA/concat.3.d.bcf /tmp/2uenORsFxA/concat.3.e.bcf /tmp/2uenORsFxA/concat.3.f.bcf .. ok test_vcf_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat -Ob -l /tmp/2uenORsFxA/concat.3.a.bcf /tmp/2uenORsFxA/concat.3.b.bcf /tmp/2uenORsFxA/concat.3.0.bcf /tmp/2uenORsFxA/concat.3.c.bcf /tmp/2uenORsFxA/concat.3.d.bcf /tmp/2uenORsFxA/concat.3.e.bcf /tmp/2uenORsFxA/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1517818981 .. ok test_naive_concat: /builddir/build/BUILD/bcftools-1.9/bcftools concat --naive /tmp/2uenORsFxA/naive_concat.0.bcf /tmp/2uenORsFxA/naive_concat.1.bcf /tmp/2uenORsFxA/naive_concat.2.bcf /tmp/2uenORsFxA/naive_concat.3.bcf /tmp/2uenORsFxA/naive_concat.4.bcf /tmp/2uenORsFxA/naive_concat.5.bcf /tmp/2uenORsFxA/naive_concat.6.bcf /tmp/2uenORsFxA/naive_concat.7.bcf /tmp/2uenORsFxA/naive_concat.8.bcf /tmp/2uenORsFxA/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/2uenORsFxA/naive_concat.0.vcf.gz /tmp/2uenORsFxA/naive_concat.1.vcf.gz /tmp/2uenORsFxA/naive_concat.2.vcf.gz /tmp/2uenORsFxA/naive_concat.3.vcf.gz /tmp/2uenORsFxA/naive_concat.4.vcf.gz /tmp/2uenORsFxA/naive_concat.5.vcf.gz /tmp/2uenORsFxA/naive_concat.6.vcf.gz /tmp/2uenORsFxA/naive_concat.7.vcf.gz /tmp/2uenORsFxA/naive_concat.8.vcf.gz /tmp/2uenORsFxA/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/2uenORsFxA/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/2uenORsFxA/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/2uenORsFxA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/2uenORsFxA/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/2uenORsFxA/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/2uenORsFxA/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/2uenORsFxA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/2uenORsFxA/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/2uenORsFxA/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/2uenORsFxA/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/2uenORsFxA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/2uenORsFxA/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/2uenORsFxA/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/2uenORsFxA/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/2uenORsFxA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/2uenORsFxA/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/2uenORsFxA/reheader.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/2uenORsFxA/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/2uenORsFxA/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/2uenORsFxA/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/2uenORsFxA/empty.bcf | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/2uenORsFxA/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/2uenORsFxA/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.9/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/2uenORsFxA/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/2uenORsFxA/rename.map -Ov /tmp/2uenORsFxA/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/2uenORsFxA/rename.map -Ob /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/check.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/convert.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/convert.hap-missing.vcf.gz 2>/dev/null .. ok test_vcf_convert: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/convert.gvcf.vcf.gz 2>/dev/null .. ok test_vcf_convert_gvcf: /builddir/build/BUILD/bcftools-1.9/bcftools view -Ob /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/consensus.1.chain.new > /dev/null 2>/dev/null; cat /tmp/2uenORsFxA/consensus.1.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/consensus.2.chain.new > /dev/null 2>/dev/null; cat /tmp/2uenORsFxA/consensus.2.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/consensus.3.chain.new > /dev/null 2>/dev/null; cat /tmp/2uenORsFxA/consensus.3.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/2uenORsFxA/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/2uenORsFxA/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.9/test/consensus.fa -H 1 -c /tmp/2uenORsFxA/consensus.4.chain.new > /dev/null 2>/dev/null; cat /tmp/2uenORsFxA/consensus.4.chain.new .. ok test_vcf_consensus: /builddir/build/BUILD/bcftools-1.9/bcftools consensus /tmp/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/2uenORsFxA/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/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/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/ENST00000301246/ENST00000301246.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000301246/ENST00000301246.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000301246/15bp-insert.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000301246/ENST00000301246.gff ... Indexed 2 transcripts, 8 exons, 7 CDSs, 5 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/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/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/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-donor4.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/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-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-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-donor7.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff ... Indexed 1 transcripts, 12 exons, 12 CDSs, 1 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000341065/splice-acceptor-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-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-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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000420670/start-stop-lost.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000420670/ENST00000420670.gff ... Indexed 1 transcripts, 4 exons, 1 CDSs, 4 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000557788/ENST00000557788.fa -g /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000557788/ENST00000557788.gff /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000557788/long-overlap-del.vcf | /builddir/build/BUILD/bcftools-1.9/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.9/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' Parsing /builddir/build/BUILD/bcftools-1.9/test/csq/ENST00000557788/ENST00000557788.gff ... Indexed 1 transcripts, 2 exons, 2 CDSs, 0 UTRs Calling... .. ok test_csq_real: /builddir/build/BUILD/bcftools-1.9/bcftools csq -f /builddir/build/BUILD/bcftools-1.9/test/csq/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/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/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/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/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/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/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/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/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 Number of tests: total .. 801 passed .. 801 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: bcftools-1.9-1.fc31.armv7hl Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.dyTTWB + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.9 + DOCDIR=/builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/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.arm/usr/share/doc/bcftools + cp -pr AUTHORS /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/share/doc/bcftools + cp -pr NEWS /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/share/doc/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.30phLA + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.9 + LICENSEDIR=/builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/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.arm/usr/share/licenses/bcftools + cp -pr LICENSE /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm/usr/share/licenses/bcftools + RPM_EC=0 ++ jobs -p + exit 0 Provides: bcftools = 1.9-1.fc31 bcftools(armv7hl-32) = 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 ld-linux-armhf.so.3 ld-linux-armhf.so.3(GLIBC_2.4) libc.so.6 libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libdl.so.2 libdl.so.2(GLIBC_2.4) libgcc_s.so.1 libgcc_s.so.1(GCC_3.5) libgsl.so.23 libgslcblas.so.0 libhts.so.2 libm.so.6 libm.so.6(GLIBC_2.23) libm.so.6(GLIBC_2.29) libm.so.6(GLIBC_2.4) libperl.so.5.30 libpthread.so.0 libpthread.so.0(GLIBC_2.4) libz.so.1 rtld(GNU_HASH) Conflicts: samtools < 1.0 Processing files: bcftools-debugsource-1.9-1.fc31.armv7hl Provides: bcftools-debugsource = 1.9-1.fc31 bcftools-debugsource(armv7hl-32) = 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.armv7hl Provides: bcftools-debuginfo = 1.9-1.fc31 bcftools-debuginfo(armv7hl-32) = 1.9-1.fc31 debuginfo(build-id) = 0bc184175e75957387b4770a2e8d6f35a2976133 debuginfo(build-id) = 194c6e6bb1f34d3855aa9940e7726e7e4e0a6702 debuginfo(build-id) = 20721e0b9a6f545037b46fe8861d098591e02948 debuginfo(build-id) = 2660e2d0c81085a55db375663e67c2ee67535c2f debuginfo(build-id) = 28f6a5b75863599435a88484edb2d3b321dca290 debuginfo(build-id) = 2d32f05bcd433f646cc680bc9236337b371df32d debuginfo(build-id) = 346858eea5fd63a4eb52f6d4accaa1d3e0bb0146 debuginfo(build-id) = 3b3633774da3533f5abfad6998e287297ec1f3af debuginfo(build-id) = 5653c01b415907611a2a559dfb5bbeba8ca2aaa2 debuginfo(build-id) = 64004b1a246f9ba4c8742bbbc23a8879c0e80c49 debuginfo(build-id) = 80a60e39ead0a8e3ec57e2ad89d3e14895a67aac debuginfo(build-id) = 81299e039631cf8583ff2317aacadc279f580933 debuginfo(build-id) = 812db623a1dee5e09fb6d9a1b081cd7b42121ca7 debuginfo(build-id) = 912c25f56cbd11bc3f8a8d74a0359dfb786d9d51 debuginfo(build-id) = 988ad390214462c536ff4967c8b04238f0d9ab73 debuginfo(build-id) = 9abb62d74175286e95ffef13d141811849e80491 debuginfo(build-id) = 9ba6aae8fed89fe15b6515a727a6afd0e83d076e debuginfo(build-id) = a4bc47bb7dd9c656193899b4fd6f0ba18da4c4e4 debuginfo(build-id) = a54e0a2254a1d8f68d7b79d5261dd3dd46af26bf debuginfo(build-id) = a9a5cb150aad7b8c032ee211e4e248f22ae43794 debuginfo(build-id) = a9bd47b18e2f108e31c28643d00126e203aa20c7 debuginfo(build-id) = aae8bc9ab46195fd6b6a02a11746793da66c5cef debuginfo(build-id) = b0a99b3525380c81a117ae03c65764167cfed6b9 debuginfo(build-id) = c437883264df69b273655cefcf7ca9c88ea27758 debuginfo(build-id) = c597d5036e29a94c4ff4498eaf653a039d7ac675 debuginfo(build-id) = cfc407a8ab027ddb49cfb8c1c0a982272b5df3d1 debuginfo(build-id) = e12cf532f63e0ba039b8eb3c657b55f7a82b42ed debuginfo(build-id) = e2f64af0697ac4ab80a8ef4b0a23cd94ce05bc66 debuginfo(build-id) = e7aa4aa6a94750a734b987795ebed6c8cf07b519 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bcftools-debugsource(armv7hl-32) = 1.9-1.fc31 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm Wrote: /builddir/build/RPMS/bcftools-1.9-1.fc31.armv7hl.rpm Wrote: /builddir/build/RPMS/bcftools-debugsource-1.9-1.fc31.armv7hl.rpm Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.9-1.fc31.armv7hl.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.q53tDE + umask 022 + cd /builddir/build/BUILD + cd bcftools-1.9 + /usr/bin/rm -rf /builddir/build/BUILDROOT/bcftools-1.9-1.fc31.arm + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0