Mock Version: 2.11
Mock Version: 2.11
Mock Version: 2.11
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64le --nodeps /builddir/build/SPECS/bcftools.spec'], chrootPath='/var/lib/mock/f35-build-29050427-3953142/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fffa188dc10>timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64le --nodeps /builddir/build/SPECS/bcftools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1626998400
Wrote: /builddir/build/SRPMS/bcftools-1.13-1.fc35.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64le --nodeps /builddir/build/SPECS/bcftools.spec'], chrootPath='/var/lib/mock/f35-build-29050427-3953142/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fffa188dc10>timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64le --nodeps /builddir/build/SPECS/bcftools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1626998400
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.p1f43b
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf bcftools-1.13
+ /usr/bin/bzip2 -dc /builddir/build/SOURCES/bcftools-1.13.tar.bz2
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd bcftools-1.13
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ sed -i '1s|/usr/bin/env perl|/usr/bin/perl|' misc/color-chrs.pl misc/demo-flt.pl misc/run-roh.pl misc/vcfutils.pl misc/plot-vcfstats
+ sed -i '1s|/usr/bin/env python3\{0,1\}|/usr/bin/python3|' misc/gff2gff.py misc/guess-ploidy.py misc/plot-roh.py
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.8FPsk1
+ umask 022
+ cd /builddir/build/BUILD
+ cd bcftools-1.13
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']'
++ find . -type f -name configure -print
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.13/configure
+ diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure
+ mv ./htslib-1.13/configure.backup ./htslib-1.13/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.13/configure
+ diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure
+ mv ./htslib-1.13/configure.backup ./htslib-1.13/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.13/configure
+ diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure
--- ./htslib-1.13/configure.backup	2021-07-07 18:06:34.000000000 +0000
+++ ./htslib-1.13/configure	2021-08-09 13:00:04.962679875 +0000
@@ -1697,7 +1697,7 @@
 #ifdef __cplusplus
 extern "C"
 #endif
-char $2 ();
+__attribute__ ((used)) char $2 ();
 /* The GNU C library defines this for functions which it implements
     to always fail with ENOSYS.  Some functions are actually named
     something starting with __ and the normal name is an alias.  */
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.13/configure
+ diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure
+ mv ./htslib-1.13/configure.backup ./htslib-1.13/configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.13/configure
+ diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure
+ mv ./htslib-1.13/configure.backup ./htslib-1.13/configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
+ ./configure --build=ppc64le-redhat-linux-gnu --host=ppc64le-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' --prefix=/usr --with-htslib=system --enable-perl-filters --enable-libgsl '--with-bcf-plugin-path=/usr/local/libexec/bcftools:$(plugindir)'
checking for ppc64le-redhat-linux-gnu-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking shared library type... plain .so
checking for library containing dlopen... none required
checking if the compiler accepts -rdynamic... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for gsl/gsl_version.h... yes
checking for library containing cblas_dgemm... -lgslcblas
checking for gsl_multifit_gradient in -lgsl... yes
checking for library containing Perl_call_pv... -lperl
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
configure: License has been changed to GPL.
Linking against the GNU scientific library requires that the resulting
binary is licensed using the GNU General Public License.  In particular,
this means you will have to follow the terms of this license in order
to distribute binary copies.  For more information see the INSTALL file.
Text of the GNU General Public License can be found in the LICENSE file,
or at http://www.gnu.org/copyleft/gpl.html
Information on the GNU Scientific Library, including the rationale for
its choice of license can be found at https://www.gnu.org/software/gsl/
+ /usr/bin/make -O -j8 V=1 VERBOSE=1
echo '#define BCFTOOLS_VERSION "1.13"' > version.h
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o tabix.o tabix.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfindex.o vcfindex.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcffilter.o vcffilter.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfquery.o vcfquery.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfisec.o vcfisec.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfsom.o vcfsom.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfview.o vcfview.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfroh.o vcfroh.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfgtcheck.o vcfgtcheck.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfconcat.o vcfconcat.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfstats.o vcfstats.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o gvcf.o gvcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcmp.o vcmp.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfcall.o vcfcall.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o mcall.o mcall.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o tsv2vcf.o tsv2vcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o reheader.o reheader.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfnorm.o vcfnorm.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfconvert.o vcfconvert.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o HMM.o HMM.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o bin.o bin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfcnv.o vcfcnv.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o hclust.o hclust.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o ploidy.o ploidy.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o version.o version.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o smpl_ilist.o smpl_ilist.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o convert.o convert.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o regidx.o regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfannotate.o vcfannotate.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o consensus.o consensus.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64  -I/usr/lib64/perl5/CORE  -c -o filter.o filter.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfbuf.o vcfbuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfsort.o vcfsort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o vcfmerge.o vcfmerge.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o cols.o cols.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o mpileup.o mpileup.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o dist.o dist.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o extsort.o extsort.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o ccall.o ccall.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o bam2bcf.o bam2bcf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o bam_sample.o bam_sample.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o em.o em.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o str_finder.o str_finder.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o kmin.o kmin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o test/test-rbuf.o test/test-rbuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o test/test-regidx.o test/test-regidx.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o prob1.o prob1.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o abuf.o abuf.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.   -DPLUGINPATH='"/usr/local/libexec/bcftools:/usr/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o polysomy.o polysomy.c
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o peakfit.o peakfit.c
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/GTsubset.so version.c plugins/GTsubset.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/allele-length.so version.c plugins/allele-length.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/add-variantkey.so version.c plugins/add-variantkey.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/check-ploidy.so version.c plugins/check-ploidy.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/GTisec.so version.c plugins/GTisec.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/af-dist.so bin.c version.c plugins/af-dist.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/counts.so version.c plugins/counts.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/check-sparsity.so version.c plugins/check-sparsity.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/dosage.so version.c plugins/dosage.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/contrast.so version.c plugins/contrast.c 
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -c -o csq.o csq.c
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/frameshifts.so version.c plugins/frameshifts.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/impute-info.so version.c plugins/impute-info.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/fixref.so version.c plugins/fixref.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/gvcfz.so version.c plugins/gvcfz.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/missing2ref.so version.c plugins/missing2ref.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/fill-tags.so version.c plugins/fill-tags.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/indel-stats.so version.c plugins/indel-stats.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/mendelian.so version.c plugins/mendelian.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/prune.so version.c plugins/prune.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/parental-origin.so version.c plugins/parental-origin.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/scatter.so version.c plugins/scatter.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/setGT.so version.c plugins/setGT.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/tag2tag.so version.c plugins/tag2tag.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/smpl-stats.so version.c plugins/smpl-stats.c 
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.   -DUSE_GPL -c -o main.o main.c
gcc -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o test/test-rbuf test/test-rbuf.o -lz  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/split.so version.c plugins/split.c 
gcc  -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz  
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/split-vep.so version.c plugins/split-vep.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/trio-stats.so version.c plugins/trio-stats.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c 
gcc -fPIC -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I.    -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64  -I/usr/lib64/perl5/CORE  -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c  
gcc -rdynamic  -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o polysomy.o peakfit.o vcfplugin.o -lhts -lm -lz   -lgsl -lgslcblas -Wl,--enable-new-dtags -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld  -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld  -fstack-protector-strong -L/usr/local/lib  -L/usr/lib64/perl5/CORE -lperl -lpthread -lresolv -ldl -lm -lcrypt -lutil -lc -lpthread
vcfcnv.c:1132:5: warning: type of 'read_AF' does not match original declaration [-Wlto-type-mismatch]
 1132 | int read_AF(bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq);
      |     ^
vcfroh.c:661:5: note: type mismatch in parameter 4
  661 | int read_AF(args_t *args, bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq)
      |     ^
vcfroh.c:661:5: note: 'read_AF' was previously declared here
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.rJ1beo
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le
++ dirname /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le
+ cd bcftools-1.13
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/bin /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/share/man/man1 /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools
/usr/bin/install -p bcftools /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/bin
/usr/bin/install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/bin
/usr/bin/install -p -m 644 doc/bcftools.1 /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/share/man/man1
/usr/bin/install -p plugins/*.so /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools
+ /usr/bin/find-debuginfo -j8 --strict-build-id -m -i --build-id-seed 1.13-1.fc35 --unique-debug-suffix -1.13-1.fc35.ppc64le --unique-debug-src-base bcftools-1.13-1.fc35.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bcftools-1.13
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/GTsubset.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/bin/bcftools
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/GTisec.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/ad-bias.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/add-variantkey.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/check-ploidy.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/af-dist.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/allele-length.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/check-sparsity.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/color-chrs.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/contrast.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/counts.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/dosage.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/fill-AN-AC.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/fill-from-fasta.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/fill-tags.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/fixploidy.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/fixref.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/frameshifts.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/guess-ploidy.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/gvcfz.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/impute-info.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/indel-stats.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/isecGT.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/mendelian.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/missing2ref.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/parental-origin.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/prune.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/remove-overlaps.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/scatter.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/setGT.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/smpl-stats.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/split-vep.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/split.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/tag2tag.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/trio-dnm2.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/trio-switch-rate.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/trio-stats.so
extracting debug info from /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/libexec/bcftools/variantkey-hex.so
original debug info size: 5952kB, size after compression: 5196kB
/usr/bin/sepdebugcrcfix: Updated 39 CRC32s, 0 CRC32s did match.
5215 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.83mWGk
+ umask 022
+ cd /builddir/build/BUILD
+ cd bcftools-1.13
+ ldd bcftools
+ grep -E '/lib(64)?/libhts\.so\.'
	libhts.so.3 => /lib64/libhts.so.3 (0x00007fff8fa60000)
+ make test
./test/test-rbuf
Inserted 1-9 starting at offset 5:
  5  6  7  8  9  0  1  2  3
  1  2  3  4  5  6  7  8  9
4th is 4
Deleting 1-2:
  7  8  9  0  1  2  3
  3  4  5  6  7  8  9
Prepending 0-8:
  8  9  0  1  2  3  4  5  6  7
  8  7  6  5  4  3  2  1  0  3
Expanding:
  8  9 10 11 12 13 14 15 16 17
  8  7  6  5  4  3  2  1  0  3
./test/test-regidx
REF_PATH=: ./test/test.pl --plugins --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-}
test_usage:
	bcftools
./test/test.pl: module IO::Pty not found; skipping usage tests
test_tabix:
	tabix /tmp/vdl1lP1Iwm/merge.a.vcf.gz 2:3199812-3199812
.. ok
test_tabix:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/vdl1lP1Iwm/merge.a.bcf 2:3199812-3199812
.. ok
test_tabix:
	tabix /tmp/vdl1lP1Iwm/merge.a.vcf.gz 1:3000151-3000151
.. ok
test_tabix:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/vdl1lP1Iwm/merge.a.bcf 1:3000151-3000151
.. ok
test_index:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/vdl1lP1Iwm/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
.. ok
test_index:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/vdl1lP1Iwm/large_chrom_csi_limit.bcf chr20:1-2147483647
.. ok
test_index:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/vdl1lP1Iwm/large_chrom_csi_limit.bcf chr20:1-2147483647
.. ok
test_index:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/vdl1lP1Iwm/large_chrom_csi_limit.vcf.gz chr20:1-2147483647
.. ok
test_index:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/vdl1lP1Iwm/large_chrom_csi_limit.bcf chr20:1-2147483647
.. ok
test_index:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/vdl1lP1Iwm/large_chrom_csi_limit.vcf.gz chr20
.. ok
test_index:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/vdl1lP1Iwm/large_chrom_csi_limit.bcf chr20
.. ok
test_index:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/vdl1lP1Iwm/large_chrom_csi_limit.bcf chr20
.. ok
test_index:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/vdl1lP1Iwm/large_chrom_csi_limit.vcf.gz chr20
.. ok
test_index:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -H /tmp/vdl1lP1Iwm/large_chrom_csi_limit.bcf chr20
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -s /tmp/vdl1lP1Iwm/idx.vcf.gz
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -s /tmp/vdl1lP1Iwm/idx.vcf.gz
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -s /tmp/vdl1lP1Iwm/idx.bcf
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/vdl1lP1Iwm/idx.vcf.gz
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/vdl1lP1Iwm/idx.vcf.gz
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/vdl1lP1Iwm/idx.vcf.gz.csi
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/vdl1lP1Iwm/idx.bcf
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/vdl1lP1Iwm/idx.bcf.csi
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -s /tmp/vdl1lP1Iwm/empty.vcf.gz
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -s /tmp/vdl1lP1Iwm/empty.vcf.gz
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -s /tmp/vdl1lP1Iwm/empty.bcf
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/vdl1lP1Iwm/empty.vcf.gz
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/vdl1lP1Iwm/empty.vcf.gz
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/vdl1lP1Iwm/empty.vcf.gz.csi
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/vdl1lP1Iwm/empty.bcf
.. ok
test_vcf_idxstats:
	/builddir/build/BUILD/bcftools-1.13/bcftools index -n /tmp/vdl1lP1Iwm/empty.bcf.csi
.. ok
test_vcf_check:
	/builddir/build/BUILD/bcftools-1.13/bcftools stats -s - /tmp/vdl1lP1Iwm/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
.. ok
test_vcf_check:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
.. ok
test_vcf_check_merge:
	/builddir/build/BUILD/bcftools-1.13/misc/plot-vcfstats -m /tmp/vdl1lP1Iwm/check.1.chk /tmp/vdl1lP1Iwm/check.2.chk /tmp/vdl1lP1Iwm/check.3.chk /tmp/vdl1lP1Iwm/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID	'
.. ok
test_vcf_stats:
	/builddir/build/BUILD/bcftools-1.13/bcftools stats -s -  /tmp/vdl1lP1Iwm/stats.a.vcf.gz /tmp/vdl1lP1Iwm/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID	'
.. ok
test_vcf_stats:
	/builddir/build/BUILD/bcftools-1.13/bcftools stats -s B  /tmp/vdl1lP1Iwm/stats.a.vcf.gz /tmp/vdl1lP1Iwm/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID	'
.. ok
test_vcf_stats:
	/builddir/build/BUILD/bcftools-1.13/bcftools stats -s -  /tmp/vdl1lP1Iwm/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID	'
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -n =2 /tmp/vdl1lP1Iwm/isec.a.vcf.gz /tmp/vdl1lP1Iwm/isec.b.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -n =2 /tmp/vdl1lP1Iwm/isec.a.vcf.gz /tmp/vdl1lP1Iwm/isec.b.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/vdl1lP1Iwm/isec.a.vcf.gz /tmp/vdl1lP1Iwm/isec.b.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/vdl1lP1Iwm/isec.a.vcf.gz /tmp/vdl1lP1Iwm/isec.b.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -n =2 -c both /tmp/vdl1lP1Iwm/isec.a.vcf.gz /tmp/vdl1lP1Iwm/isec.b.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -n =2 -c both /tmp/vdl1lP1Iwm/isec.a.vcf.gz /tmp/vdl1lP1Iwm/isec.b.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -n =2 -c any /tmp/vdl1lP1Iwm/isec.a.vcf.gz /tmp/vdl1lP1Iwm/isec.b.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -n =2 -c any /tmp/vdl1lP1Iwm/isec.a.vcf.gz /tmp/vdl1lP1Iwm/isec.b.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -C -c any /tmp/vdl1lP1Iwm/isec.a.vcf.gz /tmp/vdl1lP1Iwm/isec.b.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -C -c any /tmp/vdl1lP1Iwm/isec.a.vcf.gz /tmp/vdl1lP1Iwm/isec.b.vcf.gz
.. ok
test_vcf_isec2:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec --no-version   -T /tmp/vdl1lP1Iwm/isec.tab.gz /tmp/vdl1lP1Iwm/isec.a.vcf.gz
.. ok
test_vcf_isec2:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob  -T /tmp/vdl1lP1Iwm/isec.tab.gz /tmp/vdl1lP1Iwm/isec.a.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vdl1lP1Iwm/isec-miss.1.1.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.1.2.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.1.3.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vdl1lP1Iwm/isec-miss.1.1.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.1.2.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.1.3.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -R /builddir/build/BUILD/bcftools-1.13/test/isec-miss.1.regs.txt -n +1 /tmp/vdl1lP1Iwm/isec-miss.1.1.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.1.2.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.1.3.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.13/test/isec-miss.1.regs.txt -n +1 /tmp/vdl1lP1Iwm/isec-miss.1.1.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.1.2.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.1.3.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vdl1lP1Iwm/isec-miss.2.1.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.2.2.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.2.3.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vdl1lP1Iwm/isec-miss.2.1.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.2.2.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.2.3.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -R /builddir/build/BUILD/bcftools-1.13/test/isec-miss.1.regs.txt -n +1 /tmp/vdl1lP1Iwm/isec-miss.2.1.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.2.2.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.2.3.vcf.gz
.. ok
test_vcf_isec:
	/builddir/build/BUILD/bcftools-1.13/bcftools isec -Ob -R /builddir/build/BUILD/bcftools-1.13/test/isec-miss.1.regs.txt -n +1 /tmp/vdl1lP1Iwm/isec-miss.2.1.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.2.2.vcf.gz /tmp/vdl1lP1Iwm/isec-miss.2.3.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -i AF:join /tmp/vdl1lP1Iwm/merge.join.a.vcf.gz /tmp/vdl1lP1Iwm/merge.join.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -i AF:join /tmp/vdl1lP1Iwm/merge.join.a.vcf.gz /tmp/vdl1lP1Iwm/merge.join.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -i AF:join /tmp/vdl1lP1Iwm/merge.join.a.bcf /tmp/vdl1lP1Iwm/merge.join.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -i AF:join /tmp/vdl1lP1Iwm/merge.join.a.bcf /tmp/vdl1lP1Iwm/merge.join.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/vdl1lP1Iwm/merge.LPL.a.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.b.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.c.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/vdl1lP1Iwm/merge.LPL.a.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.b.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/vdl1lP1Iwm/merge.LPL.a.bcf /tmp/vdl1lP1Iwm/merge.LPL.b.bcf /tmp/vdl1lP1Iwm/merge.LPL.c.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/vdl1lP1Iwm/merge.LPL.a.bcf /tmp/vdl1lP1Iwm/merge.LPL.b.bcf /tmp/vdl1lP1Iwm/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 1 /tmp/vdl1lP1Iwm/merge.LPL.a.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.b.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.c.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 1 /tmp/vdl1lP1Iwm/merge.LPL.a.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.b.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 1 /tmp/vdl1lP1Iwm/merge.LPL.a.bcf /tmp/vdl1lP1Iwm/merge.LPL.b.bcf /tmp/vdl1lP1Iwm/merge.LPL.c.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 1 /tmp/vdl1lP1Iwm/merge.LPL.a.bcf /tmp/vdl1lP1Iwm/merge.LPL.b.bcf /tmp/vdl1lP1Iwm/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 2 /tmp/vdl1lP1Iwm/merge.LPL.a.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.b.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.c.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 2 /tmp/vdl1lP1Iwm/merge.LPL.a.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.b.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 2 /tmp/vdl1lP1Iwm/merge.LPL.a.bcf /tmp/vdl1lP1Iwm/merge.LPL.b.bcf /tmp/vdl1lP1Iwm/merge.LPL.c.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 2 /tmp/vdl1lP1Iwm/merge.LPL.a.bcf /tmp/vdl1lP1Iwm/merge.LPL.b.bcf /tmp/vdl1lP1Iwm/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 3 /tmp/vdl1lP1Iwm/merge.LPL.a.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.b.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.c.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 3 /tmp/vdl1lP1Iwm/merge.LPL.a.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.b.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 3 /tmp/vdl1lP1Iwm/merge.LPL.a.bcf /tmp/vdl1lP1Iwm/merge.LPL.b.bcf /tmp/vdl1lP1Iwm/merge.LPL.c.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 3 /tmp/vdl1lP1Iwm/merge.LPL.a.bcf /tmp/vdl1lP1Iwm/merge.LPL.b.bcf /tmp/vdl1lP1Iwm/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 4 /tmp/vdl1lP1Iwm/merge.LPL.a.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.b.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.c.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 4 /tmp/vdl1lP1Iwm/merge.LPL.a.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.b.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 4 /tmp/vdl1lP1Iwm/merge.LPL.a.bcf /tmp/vdl1lP1Iwm/merge.LPL.b.bcf /tmp/vdl1lP1Iwm/merge.LPL.c.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 4 /tmp/vdl1lP1Iwm/merge.LPL.a.bcf /tmp/vdl1lP1Iwm/merge.LPL.b.bcf /tmp/vdl1lP1Iwm/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 5 /tmp/vdl1lP1Iwm/merge.LPL.a.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.b.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.c.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 5 /tmp/vdl1lP1Iwm/merge.LPL.a.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.b.vcf.gz /tmp/vdl1lP1Iwm/merge.LPL.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -L 5 /tmp/vdl1lP1Iwm/merge.LPL.a.bcf /tmp/vdl1lP1Iwm/merge.LPL.b.bcf /tmp/vdl1lP1Iwm/merge.LPL.c.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -L 5 /tmp/vdl1lP1Iwm/merge.LPL.a.bcf /tmp/vdl1lP1Iwm/merge.LPL.b.bcf /tmp/vdl1lP1Iwm/merge.LPL.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/vdl1lP1Iwm/merge.a.vcf.gz /tmp/vdl1lP1Iwm/merge.b.vcf.gz /tmp/vdl1lP1Iwm/merge.c.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/vdl1lP1Iwm/merge.a.vcf.gz /tmp/vdl1lP1Iwm/merge.b.vcf.gz /tmp/vdl1lP1Iwm/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/vdl1lP1Iwm/merge.a.bcf /tmp/vdl1lP1Iwm/merge.b.bcf /tmp/vdl1lP1Iwm/merge.c.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/vdl1lP1Iwm/merge.a.bcf /tmp/vdl1lP1Iwm/merge.b.bcf /tmp/vdl1lP1Iwm/merge.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -Fx /tmp/vdl1lP1Iwm/merge.a.vcf.gz /tmp/vdl1lP1Iwm/merge.b.vcf.gz /tmp/vdl1lP1Iwm/merge.c.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -Fx /tmp/vdl1lP1Iwm/merge.a.vcf.gz /tmp/vdl1lP1Iwm/merge.b.vcf.gz /tmp/vdl1lP1Iwm/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -Fx /tmp/vdl1lP1Iwm/merge.a.bcf /tmp/vdl1lP1Iwm/merge.b.bcf /tmp/vdl1lP1Iwm/merge.c.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -Fx /tmp/vdl1lP1Iwm/merge.a.bcf /tmp/vdl1lP1Iwm/merge.b.bcf /tmp/vdl1lP1Iwm/merge.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -0 /tmp/vdl1lP1Iwm/merge.a.vcf.gz /tmp/vdl1lP1Iwm/merge.b.vcf.gz /tmp/vdl1lP1Iwm/merge.c.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -0 /tmp/vdl1lP1Iwm/merge.a.vcf.gz /tmp/vdl1lP1Iwm/merge.b.vcf.gz /tmp/vdl1lP1Iwm/merge.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -0 /tmp/vdl1lP1Iwm/merge.a.bcf /tmp/vdl1lP1Iwm/merge.b.bcf /tmp/vdl1lP1Iwm/merge.c.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -0 /tmp/vdl1lP1Iwm/merge.a.bcf /tmp/vdl1lP1Iwm/merge.b.bcf /tmp/vdl1lP1Iwm/merge.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m none /tmp/vdl1lP1Iwm/merge.2.a.vcf.gz /tmp/vdl1lP1Iwm/merge.2.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m none /tmp/vdl1lP1Iwm/merge.2.a.vcf.gz /tmp/vdl1lP1Iwm/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m none /tmp/vdl1lP1Iwm/merge.2.a.bcf /tmp/vdl1lP1Iwm/merge.2.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m none /tmp/vdl1lP1Iwm/merge.2.a.bcf /tmp/vdl1lP1Iwm/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m both /tmp/vdl1lP1Iwm/merge.2.a.vcf.gz /tmp/vdl1lP1Iwm/merge.2.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m both /tmp/vdl1lP1Iwm/merge.2.a.vcf.gz /tmp/vdl1lP1Iwm/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m both /tmp/vdl1lP1Iwm/merge.2.a.bcf /tmp/vdl1lP1Iwm/merge.2.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m both /tmp/vdl1lP1Iwm/merge.2.a.bcf /tmp/vdl1lP1Iwm/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m all /tmp/vdl1lP1Iwm/merge.2.a.vcf.gz /tmp/vdl1lP1Iwm/merge.2.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m all /tmp/vdl1lP1Iwm/merge.2.a.vcf.gz /tmp/vdl1lP1Iwm/merge.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m all /tmp/vdl1lP1Iwm/merge.2.a.bcf /tmp/vdl1lP1Iwm/merge.2.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m all /tmp/vdl1lP1Iwm/merge.2.a.bcf /tmp/vdl1lP1Iwm/merge.2.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vdl1lP1Iwm/merge.3.a.vcf.gz /tmp/vdl1lP1Iwm/merge.3.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vdl1lP1Iwm/merge.3.a.vcf.gz /tmp/vdl1lP1Iwm/merge.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vdl1lP1Iwm/merge.3.a.bcf /tmp/vdl1lP1Iwm/merge.3.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vdl1lP1Iwm/merge.3.a.bcf /tmp/vdl1lP1Iwm/merge.3.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m id /tmp/vdl1lP1Iwm/merge.4.a.vcf.gz /tmp/vdl1lP1Iwm/merge.4.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m id /tmp/vdl1lP1Iwm/merge.4.a.vcf.gz /tmp/vdl1lP1Iwm/merge.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples -m id /tmp/vdl1lP1Iwm/merge.4.a.bcf /tmp/vdl1lP1Iwm/merge.4.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples -m id /tmp/vdl1lP1Iwm/merge.4.a.bcf /tmp/vdl1lP1Iwm/merge.4.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/vdl1lP1Iwm/gvcf.merge.1.vcf.gz /tmp/vdl1lP1Iwm/gvcf.merge.2.vcf.gz /tmp/vdl1lP1Iwm/gvcf.merge.3.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/vdl1lP1Iwm/gvcf.merge.1.vcf.gz /tmp/vdl1lP1Iwm/gvcf.merge.2.vcf.gz /tmp/vdl1lP1Iwm/gvcf.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/vdl1lP1Iwm/gvcf.merge.1.bcf /tmp/vdl1lP1Iwm/gvcf.merge.2.bcf /tmp/vdl1lP1Iwm/gvcf.merge.3.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/vdl1lP1Iwm/gvcf.merge.1.bcf /tmp/vdl1lP1Iwm/gvcf.merge.2.bcf /tmp/vdl1lP1Iwm/gvcf.merge.3.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.2.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.2.b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.2.c.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.2.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.2.b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.2.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - -i SRC:join /tmp/vdl1lP1Iwm/merge.gvcf.3.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.3.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - -i SRC:join /tmp/vdl1lP1Iwm/merge.gvcf.3.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.3.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.4.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.4.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.4.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.4.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.4.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.4.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.4.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version  /tmp/vdl1lP1Iwm/merge.5.a.vcf.gz /tmp/vdl1lP1Iwm/merge.5.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob  /tmp/vdl1lP1Iwm/merge.5.a.vcf.gz /tmp/vdl1lP1Iwm/merge.5.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version  /tmp/vdl1lP1Iwm/merge.5.a.bcf /tmp/vdl1lP1Iwm/merge.5.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob  /tmp/vdl1lP1Iwm/merge.5.a.bcf /tmp/vdl1lP1Iwm/merge.5.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version  /tmp/vdl1lP1Iwm/merge.6.a.vcf.gz /tmp/vdl1lP1Iwm/merge.6.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob  /tmp/vdl1lP1Iwm/merge.6.a.vcf.gz /tmp/vdl1lP1Iwm/merge.6.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version  /tmp/vdl1lP1Iwm/merge.6.a.bcf /tmp/vdl1lP1Iwm/merge.6.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob  /tmp/vdl1lP1Iwm/merge.6.a.bcf /tmp/vdl1lP1Iwm/merge.6.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.7.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.7.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.7.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.7.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.7.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.7.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.7.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.8.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.8.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.8.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.8.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.8.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.8.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf - /tmp/vdl1lP1Iwm/merge.gvcf.8.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.8.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/vdl1lP1Iwm/merge.7.a.vcf.gz /tmp/vdl1lP1Iwm/merge.7.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/vdl1lP1Iwm/merge.7.a.vcf.gz /tmp/vdl1lP1Iwm/merge.7.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --force-samples /tmp/vdl1lP1Iwm/merge.7.a.bcf /tmp/vdl1lP1Iwm/merge.7.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --force-samples /tmp/vdl1lP1Iwm/merge.7.a.bcf /tmp/vdl1lP1Iwm/merge.7.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/vdl1lP1Iwm/merge.gvcf.9a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9c.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9d.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/vdl1lP1Iwm/merge.gvcf.9a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9c.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/vdl1lP1Iwm/merge.gvcf.9a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9b.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9c.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9d.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/vdl1lP1Iwm/merge.gvcf.9a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9b.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9c.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/vdl1lP1Iwm/merge.gvcf.9a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9c.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9d.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/vdl1lP1Iwm/merge.gvcf.9a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9c.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9d.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/vdl1lP1Iwm/merge.gvcf.9a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9b.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9c.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9d.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/vdl1lP1Iwm/merge.gvcf.9a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9b.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9c.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9d.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/vdl1lP1Iwm/merge.gvcf.9a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9c.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9d.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9e.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/vdl1lP1Iwm/merge.gvcf.9a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9c.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9d.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/vdl1lP1Iwm/merge.gvcf.9a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9b.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9c.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9d.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9e.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/vdl1lP1Iwm/merge.gvcf.9a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9b.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9c.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9d.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/vdl1lP1Iwm/merge.gvcf.9a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9c.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9d.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9e.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/vdl1lP1Iwm/merge.gvcf.9a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9c.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9d.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.9e.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/vdl1lP1Iwm/merge.gvcf.9a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9b.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9c.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9d.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9e.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --gvcf /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa -r 22:21-23 /tmp/vdl1lP1Iwm/merge.gvcf.9a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9b.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9c.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9d.bcf /tmp/vdl1lP1Iwm/merge.gvcf.9e.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version  /tmp/vdl1lP1Iwm/merge.gvcf.10.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.10.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob  /tmp/vdl1lP1Iwm/merge.gvcf.10.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version  /tmp/vdl1lP1Iwm/merge.gvcf.10.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.10.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob  /tmp/vdl1lP1Iwm/merge.gvcf.10.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -m none /tmp/vdl1lP1Iwm/merge.gvcf.10.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.10.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -m none /tmp/vdl1lP1Iwm/merge.gvcf.10.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -m none /tmp/vdl1lP1Iwm/merge.gvcf.10.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.10.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -m none /tmp/vdl1lP1Iwm/merge.gvcf.10.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/vdl1lP1Iwm/merge.gvcf.10.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.10.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/vdl1lP1Iwm/merge.gvcf.10.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/vdl1lP1Iwm/merge.gvcf.10.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.10.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/vdl1lP1Iwm/merge.gvcf.10.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/vdl1lP1Iwm/merge.gvcf.10.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.10.b.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/vdl1lP1Iwm/merge.gvcf.10.a.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.10.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/vdl1lP1Iwm/merge.gvcf.10.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.10.b.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/vdl1lP1Iwm/merge.gvcf.10.a.bcf /tmp/vdl1lP1Iwm/merge.gvcf.10.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/vdl1lP1Iwm/merge.gvcf.10.b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.10.a.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/vdl1lP1Iwm/merge.gvcf.10.b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/vdl1lP1Iwm/merge.gvcf.10.b.bcf /tmp/vdl1lP1Iwm/merge.gvcf.10.a.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa /tmp/vdl1lP1Iwm/merge.gvcf.10.b.bcf /tmp/vdl1lP1Iwm/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/vdl1lP1Iwm/merge.gvcf.10.b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.10.a.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/vdl1lP1Iwm/merge.gvcf.10.b.vcf.gz /tmp/vdl1lP1Iwm/merge.gvcf.10.a.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/vdl1lP1Iwm/merge.gvcf.10.b.bcf /tmp/vdl1lP1Iwm/merge.gvcf.10.a.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob -g /builddir/build/BUILD/bcftools-1.13/test/merge.gvcf.10.fa -m none /tmp/vdl1lP1Iwm/merge.gvcf.10.b.bcf /tmp/vdl1lP1Iwm/merge.gvcf.10.a.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version  /tmp/vdl1lP1Iwm/merge.noidx.a.vcf.gz /tmp/vdl1lP1Iwm/merge.noidx.b.vcf.gz /tmp/vdl1lP1Iwm/merge.noidx.c.vcf.gz
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob  /tmp/vdl1lP1Iwm/merge.noidx.a.vcf.gz /tmp/vdl1lP1Iwm/merge.noidx.b.vcf.gz /tmp/vdl1lP1Iwm/merge.noidx.c.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version  /tmp/vdl1lP1Iwm/merge.noidx.a.bcf /tmp/vdl1lP1Iwm/merge.noidx.b.bcf /tmp/vdl1lP1Iwm/merge.noidx.c.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob  /tmp/vdl1lP1Iwm/merge.noidx.a.bcf /tmp/vdl1lP1Iwm/merge.noidx.b.bcf /tmp/vdl1lP1Iwm/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --no-index /builddir/build/BUILD/bcftools-1.13/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.13/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.13/test/merge.noidx.c.vcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --no-index /builddir/build/BUILD/bcftools-1.13/test/merge.noidx.a.vcf /builddir/build/BUILD/bcftools-1.13/test/merge.noidx.b.vcf /builddir/build/BUILD/bcftools-1.13/test/merge.noidx.c.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge --no-version --no-index /tmp/vdl1lP1Iwm/merge.noidx.a.bcf /tmp/vdl1lP1Iwm/merge.noidx.b.bcf /tmp/vdl1lP1Iwm/merge.noidx.c.bcf
.. ok
test_vcf_merge:
	/builddir/build/BUILD/bcftools-1.13/bcftools merge -Ob --no-index /tmp/vdl1lP1Iwm/merge.noidx.a.bcf /tmp/vdl1lP1Iwm/merge.noidx.b.bcf /tmp/vdl1lP1Iwm/merge.noidx.c.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/vdl1lP1Iwm/query.string.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/vdl1lP1Iwm/query.string.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/vdl1lP1Iwm/query.string.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.string.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f '%RSX\t%VKX\n' /tmp/vdl1lP1Iwm/query.variantkey.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.variantkey.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%RSX\t%VKX\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XRI\n' -i'XRI[*]>1111'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XRF\n' -i'XRF[*]=2e6'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[2]~"H"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XGS\n' -i'XGS[*]~"H"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/vdl1lP1Iwm/view.vectors.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.vectors.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/vdl1lP1Iwm/query.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/vdl1lP1Iwm/query.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/vdl1lP1Iwm/query.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/vdl1lP1Iwm/query.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/vdl1lP1Iwm/query.2.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -i'IINT="."'  -f'%POS %IINT\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'IINT="."'  -f'%POS %IINT\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'IINT!="."' -f'%POS %IINT\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -e'IINT!="."' -f'%POS %IINT\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -e'IINT="."'  -f'%POS %IINT\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -e'IINT="."'  -f'%POS %IINT\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -i'IFLT="."'  -f'%POS %IFLT\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'IFLT="."'  -f'%POS %IFLT\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -e'IFLT="."'  -f'%POS %IFLT\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -e'IFLT="."'  -f'%POS %IFLT\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -i'ISTR="."'  -f'%POS %ISTR\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'ISTR="."'  -f'%POS %ISTR\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -e'ISTR="."'  -f'%POS %ISTR\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -e'ISTR="."'  -f'%POS %ISTR\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/vdl1lP1Iwm/filter.11.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/vdl1lP1Iwm/filter.11.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/vdl1lP1Iwm/filter.11.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/vdl1lP1Iwm/filter.11.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%LINE' /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%LINE'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/vdl1lP1Iwm/query.filter-type.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/vdl1lP1Iwm/query.filter-type.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/vdl1lP1Iwm/query.filter-type.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/vdl1lP1Iwm/query.filter-type.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/vdl1lP1Iwm/query.filter-type.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter-type.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/vdl1lP1Iwm/filter-missing-floats.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/vdl1lP1Iwm/filter-missing-floats.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/filter-missing-floats.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/vdl1lP1Iwm/missing.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/vdl1lP1Iwm/query.filter.2.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/vdl1lP1Iwm/filter.5.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/vdl1lP1Iwm/filter.5.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 |  FMT/DP="."' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 |  FMT/DP="."'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 &  FMT/GQ=589' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 &  FMT/GQ=589'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/vdl1lP1Iwm/view.filter.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.filter.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/vdl1lP1Iwm/query.filter.3.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" &  GT~"2"' /tmp/vdl1lP1Iwm/query.filter.3.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" &  GT~"2"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/vdl1lP1Iwm/query.filter.3.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS  %SAMPLE  %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/vdl1lP1Iwm/filter.5.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS  %SAMPLE  %AD\n]\n' -i'AD[:0]+AD[:1] > 12'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/vdl1lP1Iwm/query.filter.4.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.4.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.13/test/query.56.out' /tmp/vdl1lP1Iwm/view.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/view.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%ID\n' -i 'ID=@/builddir/build/BUILD/bcftools-1.13/test/query.56.out'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/vdl1lP1Iwm/query.filter.5.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/vdl1lP1Iwm/query.filter.5.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/vdl1lP1Iwm/query.filter.5.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.5.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/vdl1lP1Iwm/query.negative.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/vdl1lP1Iwm/query.negative.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/vdl1lP1Iwm/query.negative.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/vdl1lP1Iwm/query.negative.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.negative.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/vdl1lP1Iwm/query.filter.11.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/vdl1lP1Iwm/query.filter.11.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/vdl1lP1Iwm/query.filter.11.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/vdl1lP1Iwm/query.filter.11.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0' /tmp/vdl1lP1Iwm/query.pbinom.1.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.pbinom.1.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS %SAMPLE %GT %AD %PBINOM(AD)\n]' -i'phred(binom(FMT/AD))>=0'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/vdl1lP1Iwm/query.filter.6.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.6.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.7.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/vdl1lP1Iwm/query.filter.8.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/vdl1lP1Iwm/query.filter.8.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.8.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/vdl1lP1Iwm/query.filter.9.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/vdl1lP1Iwm/query.filter.9.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.9.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS  %SAMPLE  %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS  %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/vdl1lP1Iwm/query.filter.10.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS  %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS  %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/vdl1lP1Iwm/query.filter.10.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.10.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS  %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/vdl1lP1Iwm/query.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n'
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/vdl1lP1Iwm/query.filter.12.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/vdl1lP1Iwm/query.filter.12.vcf.gz
.. ok
test_vcf_query:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/query.filter.12.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -cx -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/vdl1lP1Iwm/norm.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -cx -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/vdl1lP1Iwm/norm.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -m- /tmp/vdl1lP1Iwm/norm.split.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -m- /tmp/vdl1lP1Iwm/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -m- /tmp/vdl1lP1Iwm/norm.split.2.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -m- /tmp/vdl1lP1Iwm/norm.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -m- --force /tmp/vdl1lP1Iwm/norm.split.3.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -m- --force /tmp/vdl1lP1Iwm/norm.split.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -m- /tmp/vdl1lP1Iwm/norm.split.4.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -m- /tmp/vdl1lP1Iwm/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -m- --keep-sum AD /tmp/vdl1lP1Iwm/norm.split.4.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -m- --keep-sum AD /tmp/vdl1lP1Iwm/norm.split.4.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -m- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/vdl1lP1Iwm/norm.split.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -m- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/vdl1lP1Iwm/norm.split.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -m+ /tmp/vdl1lP1Iwm/norm.merge.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -m+ /tmp/vdl1lP1Iwm/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -m+ /tmp/vdl1lP1Iwm/norm.merge.2.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -m+ /tmp/vdl1lP1Iwm/norm.merge.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -m+ /tmp/vdl1lP1Iwm/norm.merge.3.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -m+ /tmp/vdl1lP1Iwm/norm.merge.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -m+ -s /tmp/vdl1lP1Iwm/norm.merge.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -m+ -s /tmp/vdl1lP1Iwm/norm.merge.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -Nc s -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/vdl1lP1Iwm/norm.setref.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -Nc s -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/vdl1lP1Iwm/norm.setref.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/vdl1lP1Iwm/norm.telomere.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa /tmp/vdl1lP1Iwm/norm.telomere.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -d snps /tmp/vdl1lP1Iwm/norm.rmdup.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -d snps /tmp/vdl1lP1Iwm/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -d indels /tmp/vdl1lP1Iwm/norm.rmdup.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -d indels /tmp/vdl1lP1Iwm/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -d both /tmp/vdl1lP1Iwm/norm.rmdup.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -d both /tmp/vdl1lP1Iwm/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -d all /tmp/vdl1lP1Iwm/norm.rmdup.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -d all /tmp/vdl1lP1Iwm/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -d none /tmp/vdl1lP1Iwm/norm.rmdup.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -d none /tmp/vdl1lP1Iwm/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -d exact /tmp/vdl1lP1Iwm/norm.rmdup.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -d exact /tmp/vdl1lP1Iwm/norm.rmdup.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -d none /tmp/vdl1lP1Iwm/norm.rmdup.2.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -d none /tmp/vdl1lP1Iwm/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -d exact /tmp/vdl1lP1Iwm/norm.rmdup.2.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -d exact /tmp/vdl1lP1Iwm/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -d indels /tmp/vdl1lP1Iwm/norm.rmdup.2.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -d indels /tmp/vdl1lP1Iwm/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -d any /tmp/vdl1lP1Iwm/norm.rmdup.2.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -d any /tmp/vdl1lP1Iwm/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -d both /tmp/vdl1lP1Iwm/norm.rmdup.2.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -d both /tmp/vdl1lP1Iwm/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -d snps /tmp/vdl1lP1Iwm/norm.rmdup.2.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -d snps /tmp/vdl1lP1Iwm/norm.rmdup.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version   -f /builddir/build/BUILD/bcftools-1.13/test/norm.2.fa /tmp/vdl1lP1Iwm/norm.2.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob   -f /builddir/build/BUILD/bcftools-1.13/test/norm.2.fa /tmp/vdl1lP1Iwm/norm.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -c s -f /builddir/build/BUILD/bcftools-1.13/test/norm.iupac.fa /tmp/vdl1lP1Iwm/norm.iupac.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -c s -f /builddir/build/BUILD/bcftools-1.13/test/norm.iupac.fa /tmp/vdl1lP1Iwm/norm.iupac.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  -c s -f /builddir/build/BUILD/bcftools-1.13/test/norm.3.fa /tmp/vdl1lP1Iwm/norm.3.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  -c s -f /builddir/build/BUILD/bcftools-1.13/test/norm.3.fa /tmp/vdl1lP1Iwm/norm.3.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  --atomize --old-rec-tag OLD_REC /tmp/vdl1lP1Iwm/atomize.split.1.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  --atomize --old-rec-tag OLD_REC /tmp/vdl1lP1Iwm/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vdl1lP1Iwm/atomize.split.1.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vdl1lP1Iwm/atomize.split.1.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  --atomize --old-rec-tag OLD_REC /tmp/vdl1lP1Iwm/atomize.split.2.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  --atomize --old-rec-tag OLD_REC /tmp/vdl1lP1Iwm/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm --no-version  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vdl1lP1Iwm/atomize.split.2.vcf.gz
.. ok
test_vcf_norm:
	/builddir/build/BUILD/bcftools-1.13/bcftools norm -Ob  --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vdl1lP1Iwm/atomize.split.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/vdl1lP1Iwm/view.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/vdl1lP1Iwm/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -f PASS -Xks NA00003 /tmp/vdl1lP1Iwm/view.vcf.gz -r20,Y
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -f PASS -Xks NA00003 /tmp/vdl1lP1Iwm/view.vcf.gz -r20,Y | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -xs NA00003 /tmp/vdl1lP1Iwm/view.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -xs NA00003 /tmp/vdl1lP1Iwm/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/vdl1lP1Iwm/view.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/vdl1lP1Iwm/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -p /tmp/vdl1lP1Iwm/view.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -p /tmp/vdl1lP1Iwm/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -P /tmp/vdl1lP1Iwm/view.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -P /tmp/vdl1lP1Iwm/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/vdl1lP1Iwm/view.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/vdl1lP1Iwm/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -Hu /tmp/vdl1lP1Iwm/view.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -GVsnps /tmp/vdl1lP1Iwm/view.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -GVsnps /tmp/vdl1lP1Iwm/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/vdl1lP1Iwm/view.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/vdl1lP1Iwm/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -s ^NA00003 /tmp/vdl1lP1Iwm/view.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -s ^NA00003 /tmp/vdl1lP1Iwm/view.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version  /tmp/vdl1lP1Iwm/view.omitgenotypes.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob  /tmp/vdl1lP1Iwm/view.omitgenotypes.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -G /tmp/vdl1lP1Iwm/view.omitgenotypes.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -G /tmp/vdl1lP1Iwm/view.omitgenotypes.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -HG /tmp/vdl1lP1Iwm/view.omitgenotypes.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -a /tmp/vdl1lP1Iwm/many.alleles.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -a /tmp/vdl1lP1Iwm/many.alleles.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -asA /tmp/vdl1lP1Iwm/view.vectors.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -asA /tmp/vdl1lP1Iwm/view.vectors.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -asB /tmp/vdl1lP1Iwm/view.vectors.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -asB /tmp/vdl1lP1Iwm/view.vectors.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -asA /tmp/vdl1lP1Iwm/view.vectors.2.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -asA /tmp/vdl1lP1Iwm/view.vectors.2.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/vdl1lP1Iwm/view.filter.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/vdl1lP1Iwm/view.filter.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/vdl1lP1Iwm/view.filter.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/vdl1lP1Iwm/view.filter.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i'TXT0="text"' /tmp/vdl1lP1Iwm/view.filter.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -T /builddir/build/BUILD/bcftools-1.13/test/view.chrs.tab /tmp/vdl1lP1Iwm/view.chrs.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -T /builddir/build/BUILD/bcftools-1.13/test/view.chrs.tab /tmp/vdl1lP1Iwm/view.chrs.vcf.gz  | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -i 'POS>=3062917' /tmp/vdl1lP1Iwm/filter.2.vcf.gz 1:3062917-3157410
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob -i 'POS>=3062917' /tmp/vdl1lP1Iwm/filter.2.vcf.gz 1:3062917-3157410 | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/vdl1lP1Iwm/idx.1.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/vdl1lP1Iwm/idx.2.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.13/test/idx.2.bed /tmp/vdl1lP1Iwm/idx.2.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.13/test/idx.3.bed /tmp/vdl1lP1Iwm/idx.3.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -R /builddir/build/BUILD/bcftools-1.13/test/idx.4.bed /tmp/vdl1lP1Iwm/idx.4.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -Ht 2 /tmp/vdl1lP1Iwm/view-t.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -Ht 3 /tmp/vdl1lP1Iwm/view-t.vcf.gz 
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.1.vcf -H
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.1.vcf     | /builddir/build/BUILD/bcftools-1.13/bcftools view -H
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.1.vcf -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view -H
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.2.vcf -H
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.2.vcf     | /builddir/build/BUILD/bcftools-1.13/bcftools view -H
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.2.vcf -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view -H
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.3.vcf -H
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.3.vcf     | /builddir/build/BUILD/bcftools-1.13/bcftools view -H
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.4.vcf -H
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.4.vcf     | /builddir/build/BUILD/bcftools-1.13/bcftools view -H
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.4.vcf -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view -H
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.5.vcf -H
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.5.vcf     | /builddir/build/BUILD/bcftools-1.13/bcftools view -H
.. ok
test_vcf_64bit:
	/builddir/build/BUILD/bcftools-1.13/bcftools view /builddir/build/BUILD/bcftools-1.13/test/view64bit.5.vcf -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view -H
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -C5:nonmajor /tmp/vdl1lP1Iwm/view.minmaxac.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -c6:nonmajor /tmp/vdl1lP1Iwm/view.minmaxac.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -q0.3:major /tmp/vdl1lP1Iwm/view.minmaxac.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/vdl1lP1Iwm/view.filter.annovar.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/vdl1lP1Iwm/view.filter.annovar.vcf.gz 
.. ok
test_vcf_view:
	/builddir/build/BUILD/bcftools-1.13/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/vdl1lP1Iwm/view.filter.annovar.vcf.gz 
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mg0 /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mg0 /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.4.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.5.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.X.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.ped /builddir/build/BUILD/bcftools-1.13/test/mpileup.X.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.ped /builddir/build/BUILD/bcftools-1.13/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.X.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.X.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.13/test/mpileup.NA19213.NA19129.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.13/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/mpileup.NA19213.NA19129.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/mpileup.NA19213.NA19129.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -G /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -G /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.samples --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/mpileup.hwe.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.tab.gz  /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.tab.gz  /builddir/build/BUILD/bcftools-1.13/test/mpileup.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.2.tab.gz  /builddir/build/BUILD/bcftools-1.13/test/mpileup.2.vcf
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.2.tab.gz  /builddir/build/BUILD/bcftools-1.13/test/mpileup.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.vcf
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.3.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.vcf
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.4.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.vcf
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.5.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.4.vcf
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.6.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.4.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.5.vcf
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.7.tab.gz -i /builddir/build/BUILD/bcftools-1.13/test/mpileup.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.cals.1.tab.gz  /builddir/build/BUILD/bcftools-1.13/test/mpileup.cals.1.vcf
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.cals.1.tab.gz  /builddir/build/BUILD/bcftools-1.13/test/mpileup.cals.1.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.cals.2.tab.gz  /builddir/build/BUILD/bcftools-1.13/test/mpileup.cals.2.vcf
.. ok
test_vcf_call_cAls:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mA -C alleles -T /tmp/vdl1lP1Iwm/mpileup.cals.2.tab.gz  /builddir/build/BUILD/bcftools-1.13/test/mpileup.cals.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -cv /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -cv /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.X.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.ped /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.X.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.ped /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -cv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.X.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -cv --ploidy-file /builddir/build/BUILD/bcftools-1.13/test/mpileup.ploidy -S /builddir/build/BUILD/bcftools-1.13/test/mpileup.2.samples /builddir/build/BUILD/bcftools-1.13/test/mpileup.c.X.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv /builddir/build/BUILD/bcftools-1.13/test/call-G.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv /builddir/build/BUILD/bcftools-1.13/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/call-G.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -G - --group-samples-tag AD /builddir/build/BUILD/bcftools-1.13/test/call-G.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.13/test/call-G.2.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -mv -F AN_POP,AC_POP /builddir/build/BUILD/bcftools-1.13/test/call-G.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -m /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -m /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.txt /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call --no-version -m -G /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.vcf
.. ok
test_vcf_call:
	/builddir/build/BUILD/bcftools-1.13/bcftools call -Ob -m -G /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.txt -a GP,GQ /builddir/build/BUILD/bcftools-1.13/test/call.af-fixation.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'TXT0="text"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/STR="XX"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.2.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /builddir/build/BUILD/bcftools-1.13/test/view.filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.13/test/filter.1.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -mx -g2 -G2 /builddir/build/BUILD/bcftools-1.13/test/filter.1.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' -s XX /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /builddir/build/BUILD/bcftools-1.13/test/filter.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'ALT="."' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'ALT="."' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%AC[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.13/test/filter.4.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /builddir/build/BUILD/bcftools-1.13/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.13/test/filter.4.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /builddir/build/BUILD/bcftools-1.13/test/filter.4.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="A"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="A"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="RR"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="RR"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="RA"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="RA"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="AR"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="AR"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="AA"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="AA"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="aA"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="aA"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="Aa"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="HOM"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="HET"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="HET"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'GT="HAP"' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%GT]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'AD[:1]=11' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'AD[1:]=11' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%FR]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'FR[0:1]=11' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%FR]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'AD[*]="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'AD[0:0]=="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'AD[0:0]!="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS[\t%AD]\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%QUAL\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'QUAL=="."' /builddir/build/BUILD/bcftools-1.13/test/filter.5.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\t%QUAL\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'N_PASS(DP>32)=1' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /builddir/build/BUILD/bcftools-1.13/test/filter.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'F_MISSING>=1/5' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'F_MISSING>=0.2' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /builddir/build/BUILD/bcftools-1.13/test/filter.6.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%POS\n'
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.13/test/filter.7.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /builddir/build/BUILD/bcftools-1.13/test/filter.7.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.13/test/filter.9.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /builddir/build/BUILD/bcftools-1.13/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.13/test/filter.9.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /builddir/build/BUILD/bcftools-1.13/test/filter.9.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /builddir/build/BUILD/bcftools-1.13/test/filter.8.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | grep -v ^##bcftools_
.. ok
test_vcf_filter:
	/builddir/build/BUILD/bcftools-1.13/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /builddir/build/BUILD/bcftools-1.13/test/filter.10.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_sort:
	/builddir/build/BUILD/bcftools-1.13/bcftools sort -m 0 /builddir/build/BUILD/bcftools-1.13/test/sort.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok
test_vcf_sort:
	/builddir/build/BUILD/bcftools-1.13/bcftools sort -Ob -m 0 /builddir/build/BUILD/bcftools-1.13/test/sort.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok
test_vcf_sort:
	/builddir/build/BUILD/bcftools-1.13/bcftools sort -m 1000 /builddir/build/BUILD/bcftools-1.13/test/sort.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok
test_vcf_sort:
	/builddir/build/BUILD/bcftools-1.13/bcftools sort -Ob -m 1000 /builddir/build/BUILD/bcftools-1.13/test/sort.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | /builddir/build/BUILD/bcftools-1.13/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n'
.. ok
test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.13/test/regions.tab /tmp/vdl1lP1Iwm/regions.vcf.gz
.. ok
test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /builddir/build/BUILD/bcftools-1.13/test/regions.tab
.. ok
test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /builddir/build/BUILD/bcftools-1.13/test/regions.tab /tmp/vdl1lP1Iwm/regions.vcf.gz
.. ok
test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vdl1lP1Iwm/regions.tab.gz /tmp/vdl1lP1Iwm/regions.vcf.gz
.. ok
test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vdl1lP1Iwm/regions.tab.gz
.. ok
test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/vdl1lP1Iwm/regions.tab.gz /tmp/vdl1lP1Iwm/regions.vcf.gz
.. ok
test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vdl1lP1Iwm/regions.bed /tmp/vdl1lP1Iwm/regions.vcf.gz
.. ok
test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vdl1lP1Iwm/regions.bed
.. ok
test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/vdl1lP1Iwm/regions.bed /tmp/vdl1lP1Iwm/regions.vcf.gz
.. ok
test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vdl1lP1Iwm/regions.bed.gz /tmp/vdl1lP1Iwm/regions.vcf.gz
.. ok
test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/regions.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vdl1lP1Iwm/regions.bed.gz
.. ok
test_vcf_regions:
	/builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/vdl1lP1Iwm/regions.bed.gz /tmp/vdl1lP1Iwm/regions.vcf.gz
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate.hdr -c CHROM,POS,-,T_STR /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate2.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate.hdr -c CHROM,FROM,TO,T_STR /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots.vcf.gz  -c STR,ID,QUAL,FILTER /tmp/vdl1lP1Iwm/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots.vcf.gz  -c STR,ID,QUAL,FILTER /tmp/vdl1lP1Iwm/annotate.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c ID,QUAL,FILTER,INFO,FMT /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c ID,QUAL,FILTER,INFO,FMT /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate   -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.13/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob   -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /builddir/build/BUILD/bcftools-1.13/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate   -x FORMAT /builddir/build/BUILD/bcftools-1.13/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob   -x FORMAT /builddir/build/BUILD/bcftools-1.13/test/annotate3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots4.vcf.gz  -c +INFO /tmp/vdl1lP1Iwm/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots4.vcf.gz  -c +INFO /tmp/vdl1lP1Iwm/annotate4.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.13/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots4.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /builddir/build/BUILD/bcftools-1.13/test/annotate4.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.13/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots10.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /builddir/build/BUILD/bcftools-1.13/test/annotate10.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots11.tab.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.13/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots11.tab.gz  -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /builddir/build/BUILD/bcftools-1.13/test/annotate2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -x INFO -c INFO/IINT /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -x INFO -c INFO/IINT /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots11.vcf.gz  -c FMT /tmp/vdl1lP1Iwm/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots11.vcf.gz  -c FMT /tmp/vdl1lP1Iwm/annotate11.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c FMT/newGT:=GT /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots2.vcf.gz  -c FMT/newGT:=GT /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots12.vcf.gz  -c FMT/GT:=newGT /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots12.vcf.gz  -c FMT/GT:=newGT /tmp/vdl1lP1Iwm/annotate2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.13/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC /builddir/build/BUILD/bcftools-1.13/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.13/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /builddir/build/BUILD/bcftools-1.13/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.13/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots13.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /builddir/build/BUILD/bcftools-1.13/test/annotate13.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate   -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.13/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob   -x FILTER/XX,INFO/XX --force /builddir/build/BUILD/bcftools-1.13/test/annotate14.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.13/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.13/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.13/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate15.tab.gz -h /builddir/build/BUILD/bcftools-1.13/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /builddir/build/BUILD/bcftools-1.13/test/annotate15.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate   -x FILTER /builddir/build/BUILD/bcftools-1.13/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob   -x FILTER /builddir/build/BUILD/bcftools-1.13/test/annotate16.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.13/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.13/test/annotate17.1.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.13/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate17.1.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.13/test/annotate17.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate17.3.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.13/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate17.3.tab.gz  -c CHROM,BEG,END,A,B -l A:append,B:append /builddir/build/BUILD/bcftools-1.13/test/annotate17.3.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate18.1.tab.gz  -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.13/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate18.1.tab.gz  -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.13/test/annotate18.1.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate18.2.tab.gz  -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.13/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate18.2.tab.gz  -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /builddir/build/BUILD/bcftools-1.13/test/annotate18.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate19.src.vcf.gz  -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/vdl1lP1Iwm/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate19.src.vcf.gz  -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/vdl1lP1Iwm/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/vdl1lP1Iwm/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate19.src.vcf.gz  -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/vdl1lP1Iwm/annotate19.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate20.src.vcf.gz  -c  FMT/GT /tmp/vdl1lP1Iwm/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate20.src.vcf.gz  -c  FMT/GT /tmp/vdl1lP1Iwm/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate20.src.vcf.gz  -c +FMT/GT /tmp/vdl1lP1Iwm/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate20.src.vcf.gz  -c +FMT/GT /tmp/vdl1lP1Iwm/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate20.src.vcf.gz  -c -FMT/GT /tmp/vdl1lP1Iwm/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate20.src.vcf.gz  -c -FMT/GT /tmp/vdl1lP1Iwm/annotate20.dst.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate.multi.tab.gz  -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.13/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate.multi.tab.gz  -c CHROM,POS,REF,ALT,ANN -l ANN:append /builddir/build/BUILD/bcftools-1.13/test/annotate.multi.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate.missing-append.tab.gz  -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /builddir/build/BUILD/bcftools-1.13/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate.missing-append.tab.gz  -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /builddir/build/BUILD/bcftools-1.13/test/annotate.missing-append.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annots9.tab.gz  -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.13/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annots9.tab.gz  -c CHROM,POS,REF,ALT,+ID /builddir/build/BUILD/bcftools-1.13/test/annotate9.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate   --rename-annots /builddir/build/BUILD/bcftools-1.13/test/annotate21.txt /builddir/build/BUILD/bcftools-1.13/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob   --rename-annots /builddir/build/BUILD/bcftools-1.13/test/annotate21.txt /builddir/build/BUILD/bcftools-1.13/test/annotate21.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate22.vcf.gz  -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/vdl1lP1Iwm/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate22.vcf.gz  -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/vdl1lP1Iwm/annotate22.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -a /tmp/vdl1lP1Iwm/annotate23.tab.gz  -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.13/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_annotate:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate -Ob -a /tmp/vdl1lP1Iwm/annotate23.tab.gz  -c CHROM,POS,~ID,REF,ALT,INFO/END /builddir/build/BUILD/bcftools-1.13/test/annotate23.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +missing2ref --no-version /tmp/vdl1lP1Iwm/plugin1.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +missing2ref --no-version /tmp/vdl1lP1Iwm/plugin1.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/plugin1.vcf.gz -- -t . -n 0 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/plugin1.bcf -- -t . -n 0 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.vcf.gz -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.bcf -- -t q -n 0 -i 'GT~"." && FMT/DP=30 && GQ=150' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.13/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.13/test/setGT.samples.txt]="het"' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.2.vcf.gz -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.13/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.13/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.2.bcf -- -t q -n . -i 'GT[@/builddir/build/BUILD/bcftools-1.13/test/setGT.samples.txt]="het" & binom(AD[@/builddir/build/BUILD/bcftools-1.13/test/setGT.samples.txt])<0.1' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.3.vcf.gz -- -t a -n pM | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.3.bcf -- -t a -n pM | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.3.vcf.gz -- -t a -n pm | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.3.bcf -- -t a -n pm | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.3.vcf.gz -- -t a -n c:1 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.3.bcf -- -t a -n c:1 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.3.vcf.gz -- -t a -n c:"1|1" | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.3.bcf -- -t a -n c:"1|1" | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.3.vcf.gz -- -t a -n c:"m|M" | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.3.bcf -- -t a -n c:"m|M" | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.3.vcf.gz -- -t a -n c:0/1/1 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +setGT --no-version /tmp/vdl1lP1Iwm/setGT.3.bcf -- -t a -n c:0/1/1 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-AN-AC --no-version /tmp/vdl1lP1Iwm/plugin1.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-AN-AC --no-version /tmp/vdl1lP1Iwm/plugin1.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +dosage /tmp/vdl1lP1Iwm/dosage.vcf.gz -- -t PL | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +dosage /tmp/vdl1lP1Iwm/dosage.bcf -- -t PL | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +dosage /tmp/vdl1lP1Iwm/dosage.vcf.gz -- -t GL | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +dosage /tmp/vdl1lP1Iwm/dosage.bcf -- -t GL | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +dosage /tmp/vdl1lP1Iwm/dosage.vcf.gz -- -t GT | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +dosage /tmp/vdl1lP1Iwm/dosage.bcf -- -t GT | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fixploidy --no-version /tmp/vdl1lP1Iwm/fixploidy.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.13/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.13/test/fixploidy.ploidy | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fixploidy --no-version /tmp/vdl1lP1Iwm/fixploidy.bcf -- -s /builddir/build/BUILD/bcftools-1.13/test/fixploidy.samples -p /builddir/build/BUILD/bcftools-1.13/test/fixploidy.ploidy | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +guess-ploidy /tmp/vdl1lP1Iwm/view.PL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +guess-ploidy /tmp/vdl1lP1Iwm/view.PL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +guess-ploidy /tmp/vdl1lP1Iwm/view.GL.vcf.gz -vrX | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +guess-ploidy /tmp/vdl1lP1Iwm/view.GL.bcf -vrX | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +tag2tag --no-version /tmp/vdl1lP1Iwm/view.GL.vcf.gz -- -r --gl-to-pl | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +tag2tag --no-version /tmp/vdl1lP1Iwm/view.GL.bcf -- -r --gl-to-pl | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +tag2tag --no-version /tmp/vdl1lP1Iwm/view.GP.vcf.gz -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +tag2tag --no-version /tmp/vdl1lP1Iwm/view.GP.bcf -- -r --gp-to-gt -t 0.2 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +add-variantkey /tmp/vdl1lP1Iwm/query.variantkey.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +add-variantkey /tmp/vdl1lP1Iwm/query.variantkey.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +variantkey-hex /tmp/vdl1lP1Iwm/query.variantkey.vcf.gz test/ | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +variantkey-hex /tmp/vdl1lP1Iwm/query.variantkey.bcf test/ | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +allele-length /tmp/vdl1lP1Iwm/query.nucleotide.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +allele-length /tmp/vdl1lP1Iwm/query.nucleotide.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/merge.a.vcf.gz -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/merge.a.bcf -- -t AN,AC,AC_Hom,AC_Het,AC_Hemi | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/view.vcf.gz -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/view.bcf -- -t AC,AN,AF,MAF,NS | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/view.vcf.gz -- -t AC -S /builddir/build/BUILD/bcftools-1.13/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/view.bcf -- -t AC -S /builddir/build/BUILD/bcftools-1.13/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/view.vcf.gz -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.13/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/view.bcf -- -t "DP:1=int(sum(FORMAT/DP))" -S /builddir/build/BUILD/bcftools-1.13/test/fill-tags.3.smpl | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/many-alts.vcf.gz -- -t AN,AC | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/many-alts.bcf -- -t AN,AC | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-hemi.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-hemi.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-hemi.vcf.gz -- -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-hemi.bcf -- -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-hwe.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-hwe.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-hwe.vcf.gz -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-hwe.bcf -- -t 'XX:1=F_PASS(GT="alt")' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-AN0.vcf.gz -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-AN0.bcf -- -t all,END,TYPE,F_MISSING | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-VAF.vcf.gz -- -t VAF,VAF1 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-VAF.bcf -- -t VAF,VAF1 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-AD.vcf.gz -- -t 'DP:1=int(sum(AD))' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-tags --no-version /tmp/vdl1lP1Iwm/fill-tags-AD.bcf -- -t 'DP:1=int(sum(AD))' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.vcf.gz  | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.bcf  | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.vcf.gz -- -H | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.bcf -- -H | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.vcf.gz -- -Hm | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.bcf -- -Hm | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.vcf.gz -- -Hmv | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.bcf -- -Hmv | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.vcf.gz -- -Hv | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.bcf -- -Hv | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.vcf.gz -- -m | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.bcf -- -m | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.vcf.gz -- -mv | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.bcf -- -mv | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.vcf.gz -- -v | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTisec /tmp/vdl1lP1Iwm/view.bcf -- -v | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-switch-rate /tmp/vdl1lP1Iwm/trio.vcf.gz -- -p /builddir/build/BUILD/bcftools-1.13/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-switch-rate /tmp/vdl1lP1Iwm/trio.bcf -- -p /builddir/build/BUILD/bcftools-1.13/test/trio.ped | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-stats /tmp/vdl1lP1Iwm/trio-stats.vcf.gz -a 1 -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-stats /tmp/vdl1lP1Iwm/trio-stats.bcf -a 1 -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-stats /tmp/vdl1lP1Iwm/trio-stats.vcf.gz -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-stats /tmp/vdl1lP1Iwm/trio-stats.bcf -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.ped -d mendel-errors,transmitted | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +smpl-stats /tmp/vdl1lP1Iwm/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +smpl-stats /tmp/vdl1lP1Iwm/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +indel-stats /tmp/vdl1lP1Iwm/indel-stats.vcf.gz | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +indel-stats /tmp/vdl1lP1Iwm/indel-stats.bcf | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +indel-stats /tmp/vdl1lP1Iwm/indel-stats.vcf.gz  -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +indel-stats /tmp/vdl1lP1Iwm/indel-stats.bcf  -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +indel-stats /tmp/vdl1lP1Iwm/indel-stats.vcf.gz  -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +indel-stats /tmp/vdl1lP1Iwm/indel-stats.bcf  -p /builddir/build/BUILD/bcftools-1.13/test/trio-stats.2.ped | grep -v ^CMD | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/vdl1lP1Iwm/ad-bias.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/vdl1lP1Iwm/ad-bias.bcf -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/vdl1lP1Iwm/ad-bias.2.vcf.gz -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/vdl1lP1Iwm/ad-bias.2.bcf -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/vdl1lP1Iwm/ad-bias.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/vdl1lP1Iwm/ad-bias.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/vdl1lP1Iwm/ad-bias.2.vcf.gz --no-version -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +ad-bias /tmp/vdl1lP1Iwm/ad-bias.2.bcf --no-version -- -s /builddir/build/BUILD/bcftools-1.13/test/ad-bias.samples -c | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +af-dist /tmp/vdl1lP1Iwm/af-dist.vcf.gz  | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +af-dist /tmp/vdl1lP1Iwm/af-dist.bcf  | grep -v bcftools | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/vdl1lP1Iwm/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -i /tmp/vdl1lP1Iwm/fixref.2b.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/vdl1lP1Iwm/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -i /tmp/vdl1lP1Iwm/fixref.2b.vcf.gz | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/vdl1lP1Iwm/fixref.3.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/fixref.3.fa -m top | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/vdl1lP1Iwm/fixref.3.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/fixref.3.fa -m top | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/vdl1lP1Iwm/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -m ref-alt | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/vdl1lP1Iwm/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -m ref-alt | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/vdl1lP1Iwm/fixref.2a.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -m flip | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fixref /tmp/vdl1lP1Iwm/fixref.2a.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -m flip | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-from-fasta /tmp/vdl1lP1Iwm/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.13/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-from-fasta /tmp/vdl1lP1Iwm/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/aa.fa -c AA -h /builddir/build/BUILD/bcftools-1.13/test/aa.hdr -i 'TYPE="snp"' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-from-fasta /tmp/vdl1lP1Iwm/aa.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/aa.fa -c REF -N | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-from-fasta /tmp/vdl1lP1Iwm/aa.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/aa.fa -c REF -N | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-from-fasta /tmp/vdl1lP1Iwm/ref.vcf.gz -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -c REF | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +fill-from-fasta /tmp/vdl1lP1Iwm/ref.bcf -- -f /builddir/build/BUILD/bcftools-1.13/test/norm.fa -c REF | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTsubset --no-version /tmp/vdl1lP1Iwm/view.vcf.gz -- -s NA00001 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTsubset --no-version /tmp/vdl1lP1Iwm/view.bcf -- -s NA00001 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTsubset --no-version /tmp/vdl1lP1Iwm/view.vcf.gz -- -s NA00001,NA00002 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTsubset --no-version /tmp/vdl1lP1Iwm/view.bcf -- -s NA00001,NA00002 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTsubset --no-version /tmp/vdl1lP1Iwm/view.vcf.gz -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +GTsubset --no-version /tmp/vdl1lP1Iwm/view.bcf -- -s NA00001,NA00002,NA00003 | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/vdl1lP1Iwm/mendelian.vcf.gz -t mom1,dad1,child1 -md | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/vdl1lP1Iwm/mendelian.bcf -t mom1,dad1,child1 -md | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/vdl1lP1Iwm/mendelian.vcf.gz -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/vdl1lP1Iwm/mendelian.bcf -t mom1,dad1,child1 -m+ | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/vdl1lP1Iwm/mendelian.vcf.gz -t mom1,dad1,child1 -mx | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/vdl1lP1Iwm/mendelian.bcf -t mom1,dad1,child1 -mx | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/vdl1lP1Iwm/mendelian.vcf.gz -t mom1,dad1,child1 -ma | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/vdl1lP1Iwm/mendelian.bcf -t mom1,dad1,child1 -ma | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/vdl1lP1Iwm/mendelian.vcf.gz -t mom1,dad1,child1 -mu | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +mendelian /tmp/vdl1lP1Iwm/mendelian.bcf -t mom1,dad1,child1 -mu | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/vdl1lP1Iwm/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/vdl1lP1Iwm/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 a,b -1 c | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/vdl1lP1Iwm/contrast.vcf.gz -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.13/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.13/test/contrast1.txt | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/vdl1lP1Iwm/contrast.bcf -a PASSOC,FASSOC,NOVELAL,NOVELGT -0 /builddir/build/BUILD/bcftools-1.13/test/contrast0.txt -1 /builddir/build/BUILD/bcftools-1.13/test/contrast1.txt | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/vdl1lP1Iwm/contrast.1.vcf.gz -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/vdl1lP1Iwm/contrast.1.bcf -a NOVELAL,NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/vdl1lP1Iwm/contrast.1.vcf.gz -a NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +contrast /tmp/vdl1lP1Iwm/contrast.1.bcf -a NOVELGT -0 A -1 B | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.1.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.1.bcf -p proband,father,mother --ppl --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.2.vcf.gz -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.2.bcf -p proband,father,mother --ppl --dnm-tag DNM:log --force-AD | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother           | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.4.bcf -p proband,father,mother           | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.4.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.4.vcf.gz -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.4.bcf -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.5.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.5.vcf.gz -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.5.bcf -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.6.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.6.vcf.gz -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.6.bcf -p proband,father,mother           --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\t[\t%VA]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.7.bcf -p proband,father,mother --use-DNG --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.7.vcf.gz -p proband,father,mother        --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.7.bcf -p proband,father,mother        --dnm-tag DNM:log | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.8.vcf.gz -p proband,father,mother  | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.8.bcf -p proband,father,mother  | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\t[\t%VAF]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.9.vcf.gz -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.9.bcf -p 1X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.9.vcf.gz -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +trio-dnm2 /tmp/vdl1lP1Iwm/trio-dnm/trio-dnm.9.bcf -p 2X:proband,father,mother --use-NAIVE | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[\t%DNM]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +gvcfz /tmp/vdl1lP1Iwm/gvcfz.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +gvcfz /tmp/vdl1lP1Iwm/gvcfz.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +gvcfz /tmp/vdl1lP1Iwm/gvcfz.vcf.gz -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +gvcfz /tmp/vdl1lP1Iwm/gvcfz.bcf -g 'PASS:GQ>10; FLT:-' -a | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP][\t%GQ][\t%RGQ]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +gvcfz /tmp/vdl1lP1Iwm/gvcfz.2.vcf.gz -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +gvcfz /tmp/vdl1lP1Iwm/gvcfz.2.bcf -g 'PASS:GT!="alt"' -a | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%FILTER\t%END[\t%GT][\t%DP]\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +remove-overlaps /tmp/vdl1lP1Iwm/remove-overlaps.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +remove-overlaps /tmp/vdl1lP1Iwm/remove-overlaps.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +remove-overlaps /tmp/vdl1lP1Iwm/remove-overlaps.vcf.gz -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +remove-overlaps /tmp/vdl1lP1Iwm/remove-overlaps.bcf -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.vcf.gz -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.bcf -c Consequence -s worst:missense+ | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' -i'Consequence!="."' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.vcf.gz -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.bcf -s worst:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.vcf.gz -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.bcf -s primary:missense+ -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.vcf.gz -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.bcf -s primary:missense+ -f'%POS\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.2.vcf.gz -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.2.bcf -s worst -f'%POS\t%AF\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.2.vcf.gz -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.2.bcf -s worst -f'%POS\t%INFO/AF\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.3.vcf.gz -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.3.bcf -s worst -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.3.vcf.gz -s worst -f'[%POS\t%SAMPLE\t%GT\t%Consequence\n]' -i'GT="alt"' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.3.bcf -s worst -f'[%POS\t%SAMPLE\t%GT\t%Consequence\n]' -i'GT="alt"' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.bcf -t 1:14464 -f '%POS\t%CANONICAL\t%Consequence\n' -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.vcf.gz -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.bcf -t 1:14464 -f '%POS\t%CSQ\n' -A tab -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.4.vcf.gz -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.4.bcf -f '%POS\t%BCSQ\n' -a BCSQ -A tab -d | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.vcf.gz -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.bcf -c gnomAD_NFE_AF:real,ALLELE_NUM:int | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.vcf.gz -c gnomAD_NFE_AF,ALLELE_NUM          | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.bcf -c gnomAD_NFE_AF,ALLELE_NUM          | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%gnomAD_NFE_AF\t%ALLELE_NUM\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.5.vcf.gz -s :synonymous    -c Consequence | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.5.bcf -s :synonymous    -c Consequence | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.5.vcf.gz -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.5.bcf -s :synonymous -x -c Consequence | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%Consequence\n' | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.6.vcf.gz -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.6.bcf -c SAS_AF | grep ID=SAS_AF | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.6.vcf.gz -c - | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.6.bcf -c - | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.6.vcf.gz -c - -s worst | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.6.bcf -c - -s worst | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.7.vcf.gz --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.7.bcf --annotation 'ANN' -c IMPACT -i 'INFO/IMPACT[*] ~ "MODIFIER"' | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.8.vcf.gz -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.8.bcf -a BCSQ -s worst -c Consequence,amino_acid_change,BCSQ | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.8.vcf.gz -a BCSQ -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.8.bcf -a BCSQ -s worst -f '%POS\t%Consequence\t%amino_acid_change\t%BCSQ\n' | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.9.vcf.gz -a BCSQ -f '%CHROM\t%POS\t%REF\t%ALT\t%BCSQ\n' -d -A tab | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.9.bcf -a BCSQ -f '%CHROM\t%POS\t%REF\t%ALT\t%BCSQ\n' -d -A tab | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.9.vcf.gz -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split-vep /tmp/vdl1lP1Iwm/split-vep.9.bcf -a BCSQ -f '%xPOS %xConsequence\n' -p x | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +parental-origin /tmp/vdl1lP1Iwm/parental-origin.vcf.gz -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +parental-origin /tmp/vdl1lP1Iwm/parental-origin.bcf -r 20:100 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +parental-origin /tmp/vdl1lP1Iwm/parental-origin.vcf.gz -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +parental-origin /tmp/vdl1lP1Iwm/parental-origin.bcf -r 20:101 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +parental-origin /tmp/vdl1lP1Iwm/parental-origin.vcf.gz -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +parental-origin /tmp/vdl1lP1Iwm/parental-origin.bcf -r 20:102 -p proband,father,mother -t del | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +parental-origin /tmp/vdl1lP1Iwm/parental-origin.vcf.gz -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +parental-origin /tmp/vdl1lP1Iwm/parental-origin.bcf -r 20:103 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +parental-origin /tmp/vdl1lP1Iwm/parental-origin.vcf.gz -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +parental-origin /tmp/vdl1lP1Iwm/parental-origin.bcf -r 20:104 -p proband,father,mother -t dup | grep -v ^# | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 1 -a r2,LD,HD /tmp/vdl1lP1Iwm/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 1 -a r2,LD,HD /tmp/vdl1lP1Iwm/prune.1.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 1 -a r2,LD,HD /tmp/vdl1lP1Iwm/prune.2.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 1 -a r2,LD,HD /tmp/vdl1lP1Iwm/prune.2.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/vdl1lP1Iwm/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2 -a r2 -m 0.5 -f MaxR2 /tmp/vdl1lP1Iwm/prune.1.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2 -a r2 -m 0.5  /tmp/vdl1lP1Iwm/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2 -a r2 -m 0.5  /tmp/vdl1lP1Iwm/prune.1.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/vdl1lP1Iwm/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 --AF-tag AF /tmp/vdl1lP1Iwm/prune.1.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/vdl1lP1Iwm/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 --AF-tag AF -i 'GT="alt"' /tmp/vdl1lP1Iwm/prune.1.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 -N 1st /tmp/vdl1lP1Iwm/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 -N 1st /tmp/vdl1lP1Iwm/prune.1.bcf  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/vdl1lP1Iwm/prune.1.vcf.gz  | grep -v ^##bcftools_
.. ok
test_vcf_plugin:
	/builddir/build/BUILD/bcftools-1.13/bcftools +prune -w 2bp -n 1 -N rand --random-seed 1 /tmp/vdl1lP1Iwm/prune.1.bcf  | grep -v ^##bcftools_
.. ok
test_plugin_split:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/vdl1lP1Iwm/split.1.1   && cd /tmp/vdl1lP1Iwm/split.1.1  && for f in A1.vcf A2.vcf A3.vcf B1.vcf B2.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done
.. ok
test_plugin_split:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/vdl1lP1Iwm/split.1.2 -S /builddir/build/BUILD/bcftools-1.13/test/split.smpl.1.2.txt  && cd /tmp/vdl1lP1Iwm/split.1.2  && for f in A.vcf B.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done
.. ok
test_plugin_split:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/vdl1lP1Iwm/split.1.3 -S /builddir/build/BUILD/bcftools-1.13/test/split.smpl.1.3.txt  && cd /tmp/vdl1lP1Iwm/split.1.3  && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done
.. ok
test_plugin_split:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/vdl1lP1Iwm/split.1.4 -S /builddir/build/BUILD/bcftools-1.13/test/split.smpl.1.3.txt -i 'GT[0]="alt"'  && cd /tmp/vdl1lP1Iwm/split.1.4  && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done
.. ok
test_plugin_split:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/vdl1lP1Iwm/split.1.5 -S /builddir/build/BUILD/bcftools-1.13/test/split.smpl.1.3.txt -i 'GT="alt"'  && cd /tmp/vdl1lP1Iwm/split.1.5  && for f in a3.vcf b2.vcf c.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done
.. ok
test_plugin_split:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/vdl1lP1Iwm/split.1.6 -S /builddir/build/BUILD/bcftools-1.13/test/split.smpl.1.4.txt -i 'GT="alt"'  && cd /tmp/vdl1lP1Iwm/split.1.6  && for f in file1.vcf file2.vcf file3.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done
.. ok
test_plugin_split:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.1.vcf -o /tmp/vdl1lP1Iwm/split.1.7 -G /builddir/build/BUILD/bcftools-1.13/test/split.grp.1.1.txt  && cd /tmp/vdl1lP1Iwm/split.1.7  && for f in A.vcf A1.vcf A2.vcf B.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done
.. ok
test_plugin_split:
	/builddir/build/BUILD/bcftools-1.13/bcftools +split /builddir/build/BUILD/bcftools-1.13/test/split.2.vcf -o /tmp/vdl1lP1Iwm/split.2.1   && cd /tmp/vdl1lP1Iwm/split.2.1  && for f in A1_A1-1.vcf A1_A1-2.vcf A1_A1.vcf B1.vcf B2.vcf C.vcf; do echo $f; /builddir/build/BUILD/bcftools-1.13/bcftools query -l $f; /builddir/build/BUILD/bcftools-1.13/bcftools view -H $f; done
.. ok
test_plugin_scatter:
	/builddir/build/BUILD/bcftools-1.13/bcftools +scatter /builddir/build/BUILD/bcftools-1.13/test/scatter.1.vcf -o /tmp/vdl1lP1Iwm/scatter.1.1 -n 3 && cd /tmp/vdl1lP1Iwm/scatter.1.1 && cat 0.vcf 1.vcf 2.vcf | grep -v ^##
.. ok
test_plugin_scatter:
	/builddir/build/BUILD/bcftools-1.13/bcftools +scatter /builddir/build/BUILD/bcftools-1.13/test/scatter.1.vcf -o /tmp/vdl1lP1Iwm/scatter.1.2 -s 21,22 && cd /tmp/vdl1lP1Iwm/scatter.1.2 && cat 21.vcf 22.vcf | grep -v ^##
.. ok
test_plugin_scatter:
	/builddir/build/BUILD/bcftools-1.13/bcftools +scatter /builddir/build/BUILD/bcftools-1.13/test/scatter.1.vcf -o /tmp/vdl1lP1Iwm/scatter.1.3 -s 21,22 -x X && cd /tmp/vdl1lP1Iwm/scatter.1.3 && cat 21.vcf 22.vcf X.vcf | grep -v ^##
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version   /tmp/vdl1lP1Iwm/concat.1.a.vcf.gz /tmp/vdl1lP1Iwm/concat.1.b.vcf.gz
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob   /tmp/vdl1lP1Iwm/concat.1.a.vcf.gz /tmp/vdl1lP1Iwm/concat.1.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version   /tmp/vdl1lP1Iwm/concat.1.a.bcf /tmp/vdl1lP1Iwm/concat.1.b.bcf
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob   /tmp/vdl1lP1Iwm/concat.1.a.bcf /tmp/vdl1lP1Iwm/concat.1.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -a  /tmp/vdl1lP1Iwm/concat.2.a.vcf.gz /tmp/vdl1lP1Iwm/concat.2.b.vcf.gz
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -a  /tmp/vdl1lP1Iwm/concat.2.a.vcf.gz /tmp/vdl1lP1Iwm/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -a  /tmp/vdl1lP1Iwm/concat.2.a.bcf /tmp/vdl1lP1Iwm/concat.2.b.bcf
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -a  /tmp/vdl1lP1Iwm/concat.2.a.bcf /tmp/vdl1lP1Iwm/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -aD  /tmp/vdl1lP1Iwm/concat.2.a.vcf.gz /tmp/vdl1lP1Iwm/concat.2.b.vcf.gz
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -aD  /tmp/vdl1lP1Iwm/concat.2.a.vcf.gz /tmp/vdl1lP1Iwm/concat.2.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -aD  /tmp/vdl1lP1Iwm/concat.2.a.bcf /tmp/vdl1lP1Iwm/concat.2.b.bcf
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -aD  /tmp/vdl1lP1Iwm/concat.2.a.bcf /tmp/vdl1lP1Iwm/concat.2.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -l  /tmp/vdl1lP1Iwm/concat.3.a.vcf.gz /tmp/vdl1lP1Iwm/concat.3.b.vcf.gz /tmp/vdl1lP1Iwm/concat.3.0.vcf.gz /tmp/vdl1lP1Iwm/concat.3.c.vcf.gz /tmp/vdl1lP1Iwm/concat.3.d.vcf.gz /tmp/vdl1lP1Iwm/concat.3.e.vcf.gz /tmp/vdl1lP1Iwm/concat.3.f.vcf.gz
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -l  /tmp/vdl1lP1Iwm/concat.3.a.vcf.gz /tmp/vdl1lP1Iwm/concat.3.b.vcf.gz /tmp/vdl1lP1Iwm/concat.3.0.vcf.gz /tmp/vdl1lP1Iwm/concat.3.c.vcf.gz /tmp/vdl1lP1Iwm/concat.3.d.vcf.gz /tmp/vdl1lP1Iwm/concat.3.e.vcf.gz /tmp/vdl1lP1Iwm/concat.3.f.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -l  /tmp/vdl1lP1Iwm/concat.3.a.bcf /tmp/vdl1lP1Iwm/concat.3.b.bcf /tmp/vdl1lP1Iwm/concat.3.0.bcf /tmp/vdl1lP1Iwm/concat.3.c.bcf /tmp/vdl1lP1Iwm/concat.3.d.bcf /tmp/vdl1lP1Iwm/concat.3.e.bcf /tmp/vdl1lP1Iwm/concat.3.f.bcf
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -l  /tmp/vdl1lP1Iwm/concat.3.a.bcf /tmp/vdl1lP1Iwm/concat.3.b.bcf /tmp/vdl1lP1Iwm/concat.3.0.bcf /tmp/vdl1lP1Iwm/concat.3.c.bcf /tmp/vdl1lP1Iwm/concat.3.d.bcf /tmp/vdl1lP1Iwm/concat.3.e.bcf /tmp/vdl1lP1Iwm/concat.3.f.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
Random seed for test_naive_concat: 2199505317
.. ok
test_naive_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat --naive-force /tmp/vdl1lP1Iwm/naive_concat.0.bcf /tmp/vdl1lP1Iwm/naive_concat.1.bcf /tmp/vdl1lP1Iwm/naive_concat.2.bcf /tmp/vdl1lP1Iwm/naive_concat.3.bcf /tmp/vdl1lP1Iwm/naive_concat.4.bcf /tmp/vdl1lP1Iwm/naive_concat.5.bcf /tmp/vdl1lP1Iwm/naive_concat.6.bcf /tmp/vdl1lP1Iwm/naive_concat.7.bcf /tmp/vdl1lP1Iwm/naive_concat.8.bcf /tmp/vdl1lP1Iwm/naive_concat.9.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view -H
.. ok
test_naive_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat --naive /tmp/vdl1lP1Iwm/naive_concat.0.vcf.gz /tmp/vdl1lP1Iwm/naive_concat.1.vcf.gz /tmp/vdl1lP1Iwm/naive_concat.2.vcf.gz /tmp/vdl1lP1Iwm/naive_concat.3.vcf.gz /tmp/vdl1lP1Iwm/naive_concat.4.vcf.gz /tmp/vdl1lP1Iwm/naive_concat.5.vcf.gz /tmp/vdl1lP1Iwm/naive_concat.6.vcf.gz /tmp/vdl1lP1Iwm/naive_concat.7.vcf.gz /tmp/vdl1lP1Iwm/naive_concat.8.vcf.gz /tmp/vdl1lP1Iwm/naive_concat.9.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view -H
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -l  /tmp/vdl1lP1Iwm/concat.4.a.vcf.gz /tmp/vdl1lP1Iwm/concat.4.b.vcf.gz
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -l  /tmp/vdl1lP1Iwm/concat.4.a.vcf.gz /tmp/vdl1lP1Iwm/concat.4.b.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat --no-version -l  /tmp/vdl1lP1Iwm/concat.4.a.bcf /tmp/vdl1lP1Iwm/concat.4.b.bcf
.. ok
test_vcf_concat:
	/builddir/build/BUILD/bcftools-1.13/bcftools concat -Ob -l  /tmp/vdl1lP1Iwm/concat.4.a.bcf /tmp/vdl1lP1Iwm/concat.4.b.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.hdr /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.hdr /tmp/vdl1lP1Iwm/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /tmp/vdl1lP1Iwm/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.hdr /tmp/vdl1lP1Iwm/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /tmp/vdl1lP1Iwm/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.hdr | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples /tmp/vdl1lP1Iwm/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /tmp/vdl1lP1Iwm/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples /tmp/vdl1lP1Iwm/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /tmp/vdl1lP1Iwm/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples2 /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples2 /tmp/vdl1lP1Iwm/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /tmp/vdl1lP1Iwm/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples2 /tmp/vdl1lP1Iwm/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /tmp/vdl1lP1Iwm/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples2 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples3 /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples3 /tmp/vdl1lP1Iwm/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /tmp/vdl1lP1Iwm/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples3 /tmp/vdl1lP1Iwm/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /tmp/vdl1lP1Iwm/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples3 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples4 /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.13/test/reheader.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples4 /tmp/vdl1lP1Iwm/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /tmp/vdl1lP1Iwm/reheader.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples4 /tmp/vdl1lP1Iwm/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /tmp/vdl1lP1Iwm/reheader.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -s /builddir/build/BUILD/bcftools-1.13/test/reheader.samples4 | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.empty.hdr /builddir/build/BUILD/bcftools-1.13/test/empty.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /builddir/build/BUILD/bcftools-1.13/test/empty.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.empty.hdr /tmp/vdl1lP1Iwm/empty.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /tmp/vdl1lP1Iwm/empty.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.empty.hdr /tmp/vdl1lP1Iwm/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	cat /tmp/vdl1lP1Iwm/empty.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.empty.hdr | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -f /builddir/build/BUILD/bcftools-1.13/test/reheader.fai /builddir/build/BUILD/bcftools-1.13/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -f /builddir/build/BUILD/bcftools-1.13/test/reheader.fai /tmp/vdl1lP1Iwm/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -f /builddir/build/BUILD/bcftools-1.13/test/reheader.fai /tmp/vdl1lP1Iwm/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.13/test/reheader.fai /builddir/build/BUILD/bcftools-1.13/test/reheader.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.13/test/reheader.fai /tmp/vdl1lP1Iwm/reheader.2.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_vcf_reheader:
	/builddir/build/BUILD/bcftools-1.13/bcftools reheader -h /builddir/build/BUILD/bcftools-1.13/test/reheader.2.hdr -f /builddir/build/BUILD/bcftools-1.13/test/reheader.fai /tmp/vdl1lP1Iwm/reheader.2.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools view --no-version
.. ok
test_rename_chrs:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate --rename-chrs /tmp/vdl1lP1Iwm/rename.map -Ov /tmp/vdl1lP1Iwm/annotate.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM\t%POS\n'
.. ok
test_rename_chrs:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate --rename-chrs /tmp/vdl1lP1Iwm/rename.map -Ob /tmp/vdl1lP1Iwm/annotate.bcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM\t%POS\n'
.. ok
test_rename_chrs:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate --rename-chrs /tmp/vdl1lP1Iwm/rename.map -Ov /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM\t%POS\n'
.. ok
test_rename_chrs:
	/builddir/build/BUILD/bcftools-1.13/bcftools annotate --rename-chrs /tmp/vdl1lP1Iwm/rename.map -Ob /builddir/build/BUILD/bcftools-1.13/test/annotate.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%CHROM\t%POS\n'
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. /tmp/vdl1lP1Iwm/convert.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,.
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- /tmp/vdl1lP1Iwm/convert.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,-
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --tag PL /tmp/vdl1lP1Iwm/convert.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --tag PL
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --tag PL /tmp/vdl1lP1Iwm/convert.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --tag PL
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --vcf-ids /tmp/vdl1lP1Iwm/check.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --vcf-ids
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --vcf-ids /tmp/vdl1lP1Iwm/check.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --vcf-ids
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --chrom /tmp/vdl1lP1Iwm/check.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --chrom
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --chrom /tmp/vdl1lP1Iwm/check.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --chrom
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --chrom --vcf-ids /tmp/vdl1lP1Iwm/check.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g -,. --chrom --vcf-ids
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --chrom --vcf-ids /tmp/vdl1lP1Iwm/check.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/check.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -g .,- --chrom --vcf-ids
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -h -,.,. /tmp/vdl1lP1Iwm/convert.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -h -,.,.
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -h .,-,. /tmp/vdl1lP1Iwm/convert.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -h .,-,.
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -h .,.,- /tmp/vdl1lP1Iwm/convert.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert -h .,.,-
.. ok
test_vcf_convert_hls2vcf:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -H /builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.samples | grep -v ^##
.. ok
test_vcf_convert_hls2vcf:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -H /builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##
.. ok
test_vcf_convert_hls2vcf:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert --vcf-ids -H /builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.samples | grep -v ^##
.. ok
test_vcf_convert_hls2vcf:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert --vcf-ids -H /builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.legend,/builddir/build/BUILD/bcftools-1.13/test/convert.hls.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.samples | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert --hapsample2vcf /builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.samples | grep -v ^##
.. ok
test_vcf_convert_hs2vcf:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert --vcf-ids --hapsample2vcf /builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.hap,/builddir/build/BUILD/bcftools-1.13/test/convert.hs.gt.samples -Ou | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert --hapsample -,. /tmp/vdl1lP1Iwm/convert.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert --hapsample -,.
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert --hapsample .,- /tmp/vdl1lP1Iwm/convert.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/convert.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert --hapsample .,-
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert --haplegendsample -,.,. /tmp/vdl1lP1Iwm/convert.hap-missing.vcf.gz
.. ok
test_vcf_convert:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/convert.hap-missing.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert --haplegendsample -,.,.
.. ok
test_vcf_convert_gvcf:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa /tmp/vdl1lP1Iwm/convert.gvcf.vcf.gz
.. ok
test_vcf_convert_gvcf:
	/builddir/build/BUILD/bcftools-1.13/bcftools view -Ob /tmp/vdl1lP1Iwm/convert.gvcf.vcf.gz | /builddir/build/BUILD/bcftools-1.13/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /builddir/build/BUILD/bcftools-1.13/test/gvcf.fa | grep -v ^##bcftools
.. ok
test_vcf_convert_tsv2vcf:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert --no-version  -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.13/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.13/test/convert.23andme
.. ok
test_vcf_convert_tsv2vcf:
	/builddir/build/BUILD/bcftools-1.13/bcftools convert -Ou  -c ID,CHROM,POS,AA -s SAMPLE1 -f /builddir/build/BUILD/bcftools-1.13/test/23andme.fa --tsv2vcf /builddir/build/BUILD/bcftools-1.13/test/convert.23andme | /builddir/build/BUILD/bcftools-1.13/bcftools view | grep -v ^##bcftools_
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa  -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab 
.. ok
test_vcf_consensus_chain:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa  -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab -c /tmp/vdl1lP1Iwm/consensus.1.chain.new >/dev/null; cat /tmp/vdl1lP1Iwm/consensus.1.chain.new
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab 
.. ok
test_vcf_consensus_chain:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -H 1 -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab -c /tmp/vdl1lP1Iwm/consensus.2.chain.new >/dev/null; cat /tmp/vdl1lP1Iwm/consensus.2.chain.new
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab 
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab --mask-with X -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab --mask-with lc  
.. ok
test_vcf_consensus_chain:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -I -m /builddir/build/BUILD/bcftools-1.13/test/consensus.tab -c /tmp/vdl1lP1Iwm/consensus.3.chain.new >/dev/null; cat /tmp/vdl1lP1Iwm/consensus.3.chain.new
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -H 1  
.. ok
test_vcf_consensus_chain:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -H 1  -c /tmp/vdl1lP1Iwm/consensus.4.chain.new >/dev/null; cat /tmp/vdl1lP1Iwm/consensus.4.chain.new
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus2.fa -H 1  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus2.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus2.fa -H 2  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/empty.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa   
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus2.fa -H 2 -M "?"  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus3.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus2.fa -H 2 -M "?" -p xx_  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus4.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus2.fa   
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus5.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus5.fa --haplotype LA  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus6.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus6.fa   
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus7.fa -H 2  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus7.fa -H 2pIu  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus7.fa -H 1  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus7.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus7.fa -H 1pIu  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa   
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -a .  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -a . -i 'type="snp" || type="ref"'  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -a . -i 'ALT!="<DEL>"'  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -a . -e 'MinDP>15'  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus8.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -a . -e 'MinDP<15'  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.9.1.fa -H A  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.9.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.9.2.fa -H A  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.9.1.fa -H A  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.10.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.9.2.fa -H A  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.11.fa -s smpl  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.11.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.11.fa -s smpl -a N  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.12.fa   
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.13.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.13.fa   
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.14.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.14.fa   
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.12.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.12.fa --mark-del - --mark-ins uc --mark-snv uc  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.15.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -I  
.. ok
test_vcf_consensus:
	/builddir/build/BUILD/bcftools-1.13/bcftools consensus /tmp/vdl1lP1Iwm/consensus.16.vcf.gz -f /builddir/build/BUILD/bcftools-1.13/test/consensus.fa -H I  
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -b /tmp/vdl1lP1Iwm/mpileup.bam.list --no-version | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob -b /tmp/vdl1lP1Iwm/mpileup.bam.urllist | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -b /tmp/vdl1lP1Iwm/mpileup.cram.list --no-version | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob -b /tmp/vdl1lP1Iwm/mpileup.cram.urllist | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -r17:100-150 -S ^/builddir/build/BUILD/bcftools-1.13/test/mplp.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -S /builddir/build/BUILD/bcftools-1.13/test/mplp.9.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.13/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.13/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.13/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -t17:100-150 -G /builddir/build/BUILD/bcftools-1.13/test/mplp.10.samples -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.1.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.2.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup  -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup  -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup  -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup  -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s HG00102 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -s ^HG99999 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.bam /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -G /builddir/build/BUILD/bcftools-1.13/test/mplp.11.rgs -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.ref.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.3.cram /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup.4.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.1.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/indel-AD.2.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.bam | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.fa /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_mpileup:
	/builddir/build/BUILD/bcftools-1.13/bcftools mpileup -a INFO/SCR,FMT/SCR -f /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.fa -Ob /builddir/build/BUILD/bcftools-1.13/test/mpileup/mpileup-SCR.cram | /builddir/build/BUILD/bcftools-1.13/bcftools view  | grep -v ^##bcftools | grep -v ^##reference
.. ok
test_csq:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq.gff3 /builddir/build/BUILD/bcftools-1.13/test/csq.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq.chr.gff3 /builddir/build/BUILD/bcftools-1.13/test/csq.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq.2.gff /builddir/build/BUILD/bcftools-1.13/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok
test_csq:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq.2.gff --ncsq 64 /builddir/build/BUILD/bcftools-1.13/test/csq.2.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000230048/ENST00000230048.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000230048/ENST00000230048.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000230048/start-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000528237/ENST00000528237.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000528237/ENST00000528237.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0003/EDUMMY0003.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0003/EDUMMY0003.gff /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0003/long-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420670/segfault.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420670/ENST00000420670.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420670/ENST00000420670.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420670/start-stop-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0002/EDUMMY0002.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0002/EDUMMY0002.gff /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0002/boundaries.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000382647/ENST00000382647.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000382647/ENST00000382647.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000303039/ENST00000303039.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000303039/ENST00000303039.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000303039/not-a-stop.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000593942/ENST00000593942.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000593942/ENST00000593942.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000593942/last-codon-deletion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/start-lost-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/ENST00000218032.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000218032/start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000368801.2/ENST00000368801.2.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000368801.2/start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000413103/ENST00000413103.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000413103/ENST00000413103.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000413103/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000557788/ENST00000557788.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000557788/ENST00000557788.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000557788/long-overlap-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000390520/ENST00000390520.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000390520/ENST00000390520.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000390520/deletion-overlap.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.13/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.13/test/csq/EMN908947 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000263103-INS/insertions.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000409523/ENST00000409523.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000409523/ENST00000409523.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000409523/long-overlapping-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000271583/ENST00000271583.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000271583/ENST00000271583.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000271583/splice-acceptor.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000410009 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000410009/ENST00000410009.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000410009/ENST00000410009.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000410009/frameshift.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000436063/ENST00000436063.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000436063/ENST00000436063.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000436063/insert-before-utr.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249/ENST00000318249.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249/ENST00000318249.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249/start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000518414/ENST00000518414.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000518414/ENST00000518414.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000400151/ENST00000400151.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000400151/ENST00000400151.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000400151/long-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0001/EDUMMY0001.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0001/EDUMMY0001.gff /builddir/build/BUILD/bcftools-1.13/test/csq/EDUMMY0001/starts-with-1.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000573314/ENST00000573314.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000573314/ENST00000573314.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000373833/ENST00000373833.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000373833/ENST00000373833.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000373833/boundary-insertion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.13/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.13/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.13/test/csq/ENSMUST00000121418 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520868/ENST00000520868.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520868/ENST00000520868.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520868/long-deletion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420190/ENST00000420190.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420190/ENST00000420190.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000420190/abort-in-csq-push.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520795/ENST00000520795.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520795/ENST00000520795.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000520795/long-inside-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000378322/ENST00000378322.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000378322/ENST00000378322.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000378322/end-overlap-tscript.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000624631/ENST00000624631.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000624631/ENST00000624631.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000624631/ambiguous.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000375992/ENST00000375992.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000375992/ENST00000375992.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249.2/ENST00000318249.2.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000227471/ENST00000227471.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000227471/ENST00000227471.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000368801/ENST00000368801.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000368801/ENST00000368801.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000368801/compound-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000479739/ENST00000479739.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000479739/ENST00000479739.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000479739/short-cds-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000448695/ENST00000448695.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000448695/ENST00000448695.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000542803/ENST00000542803.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000542803/ENST00000542803.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000542803/splice-region.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/frame2.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/frame3.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/frame1.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/ENST00000341065.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000301246/ENST00000301246.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000301246/ENST00000301246.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000301246/15bp-insert.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000519442/ENST00000519442.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000519442/ENST00000519442.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000519442/synon-splice-region-del.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/snps.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/ENST00000423372.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000423372/insert3.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000294661/ENST00000294661.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000294661/ENST00000294661.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000294661/non-coding-boundary.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000545279/ENST00000545279.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000545279/ENST00000545279.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000545279/splice-region-insert.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000357367/ENST00000357367.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000357367/ENST00000357367.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000357367/stop-retained.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000381157/ENST00000381157.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000381157/ENST00000381157.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000381157/haploid-diploid.vcf | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000295641/ENST00000295641.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000295641/ENST00000295641.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000295641/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	cd /builddir/build/BUILD/bcftools-1.13/test/csq/ENSMUST00000133836 && /builddir/build/BUILD/bcftools-1.13/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENSG00000173376/ENSG00000173376.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENSG00000173376/ENSG00000173376.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENSG00000173376/synon.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000543077/ENST00000543077.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000543077/ENST00000543077.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000543077/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000536784/ENST00000536784.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000536784/ENST00000536784.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000536784/not-a-start-lost.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000256452/ENST00000256452.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000256452/ENST00000256452.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000256452/intron.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_csq_real:
	/builddir/build/BUILD/bcftools-1.13/bcftools csq -l -f /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000329454/ENST00000329454.fa -g /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000329454/ENST00000329454.gff /builddir/build/BUILD/bcftools-1.13/test/csq/ENST00000329454/boundary-deletion.vcf | /builddir/build/BUILD/bcftools-1.13/test/csq/sort-csq | /builddir/build/BUILD/bcftools-1.13/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n'
.. ok
test_roh:
	/builddir/build/BUILD/bcftools-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^#
.. ok
test_roh:
	/builddir/build/BUILD/bcftools-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.13/test/roh.1.tab.gz| grep -v ^#
.. ok
test_roh:
	/builddir/build/BUILD/bcftools-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/test/roh.1.vcf.gz -Or -G30 --AF-file /builddir/build/BUILD/bcftools-1.13/test/roh.1.tab.gz --ignore-homref| grep -v ^#
.. ok
test_roh:
	/builddir/build/BUILD/bcftools-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^#
.. ok
test_roh:
	/builddir/build/BUILD/bcftools-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^#
.. ok
test_roh:
	/builddir/build/BUILD/bcftools-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^#
.. ok
test_roh:
	/builddir/build/BUILD/bcftools-1.13/bcftools roh /builddir/build/BUILD/bcftools-1.13/test/roh.1.vcf.gz     -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^#
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 /tmp/vdl1lP1Iwm/gtcheck.1.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u GT,GT /tmp/vdl1lP1Iwm/gtcheck.1.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u GT,PL /tmp/vdl1lP1Iwm/gtcheck.1.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u PL,GT /tmp/vdl1lP1Iwm/gtcheck.1.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u PL,PL /tmp/vdl1lP1Iwm/gtcheck.1.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -p s1,s1 /tmp/vdl1lP1Iwm/gtcheck.1.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 /tmp/vdl1lP1Iwm/gtcheck.2.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0  /tmp/vdl1lP1Iwm/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/vdl1lP1Iwm/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.13/test/gtcheck.3.pairs /tmp/vdl1lP1Iwm/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u PL /tmp/vdl1lP1Iwm/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 --n-matches 4 /tmp/vdl1lP1Iwm/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO  | sort
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/vdl1lP1Iwm/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/vdl1lP1Iwm/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/vdl1lP1Iwm/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/vdl1lP1Iwm/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/vdl1lP1Iwm/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -p B,C,B,D /tmp/vdl1lP1Iwm/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u GT,GT -H /tmp/vdl1lP1Iwm/gtcheck.1.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u GT,PL -H /tmp/vdl1lP1Iwm/gtcheck.1.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u PL,GT -H /tmp/vdl1lP1Iwm/gtcheck.1.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -u PL,PL -H /tmp/vdl1lP1Iwm/gtcheck.1.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.13/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/vdl1lP1Iwm/gtcheck.4.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -e 0 -P /builddir/build/BUILD/bcftools-1.13/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/vdl1lP1Iwm/gtcheck.4.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -u GT -e 30 /tmp/vdl1lP1Iwm/gtcheck.1.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/vdl1lP1Iwm/gtcheck.1.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -u GT -e 300 /tmp/vdl1lP1Iwm/gtcheck.1.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck -u PL -e 30 /tmp/vdl1lP1Iwm/gtcheck.3.vcf.gz  | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck  /tmp/vdl1lP1Iwm/gtcheck.ntop.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck --n-matches 2 /tmp/vdl1lP1Iwm/gtcheck.ntop.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO 
.. ok
test_gtcheck:
	/builddir/build/BUILD/bcftools-1.13/bcftools gtcheck  /tmp/vdl1lP1Iwm/gtcheck.5.vcf.gz -g /tmp/vdl1lP1Iwm/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time
.. ok
Number of tests:
    total   .. 1542
    passed  .. 1542
    failed  .. 0
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: bcftools-1.13-1.fc35.ppc64le
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.XolqM6
+ umask 022
+ cd /builddir/build/BUILD
+ cd bcftools-1.13
+ DOCDIR=/builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/share/doc/bcftools
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/share/doc/bcftools
+ cp -pr AUTHORS /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/share/doc/bcftools
+ cp -pr NEWS /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/share/doc/bcftools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.bZfY2o
+ umask 022
+ cd /builddir/build/BUILD
+ cd bcftools-1.13
+ LICENSEDIR=/builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/share/licenses/bcftools
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/share/licenses/bcftools
+ cp -pr LICENSE /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le/usr/share/licenses/bcftools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: bcftools = 1.13-1.fc35 bcftools(ppc-64) = 1.13-1.fc35
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl /usr/bin/python3 libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libgsl.so.25()(64bit) libgslcblas.so.0()(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libperl.so.5.34()(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Conflicts: samtools < 1.0
Processing files: bcftools-debugsource-1.13-1.fc35.ppc64le
Provides: bcftools-debugsource = 1.13-1.fc35 bcftools-debugsource(ppc-64) = 1.13-1.fc35
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: bcftools-debuginfo-1.13-1.fc35.ppc64le
Provides: bcftools-debuginfo = 1.13-1.fc35 bcftools-debuginfo(ppc-64) = 1.13-1.fc35 debuginfo(build-id) = 1910f2cf3d9dc57280fe70230f0ccb9ee679ba5c debuginfo(build-id) = 1a995a591cd07303165edb2febe8cbe20891debd debuginfo(build-id) = 1ada0550b5599fd4cfc78cbf49d93c41d6576565 debuginfo(build-id) = 1aec03f4d0844ad237ba2e9c3899b12d554ac610 debuginfo(build-id) = 1d760d18dc643e3298ed9ba520894705a9d4930f debuginfo(build-id) = 2c1f7e49267648608254c6d98a304c74739f1e74 debuginfo(build-id) = 2c4762b593bc2bc08ea79e7098bc3b0847bfca2f debuginfo(build-id) = 2f1fe6999b4fe8838fa9d9454be6b423bd187904 debuginfo(build-id) = 3174155bfa6ff5ec0e73ad8e73b6fe52586b686e debuginfo(build-id) = 336ca37fca08072e1b38f6cf6f53354569175e43 debuginfo(build-id) = 3900b7c865b649f1de2b6de63aa6d56ec97a5438 debuginfo(build-id) = 3b3d11cd58901f09047e2fba9ca50690480c4ce7 debuginfo(build-id) = 414fc176602d17d152fbe3fcfa12ffcc5165d0f9 debuginfo(build-id) = 4cd2d3bf69dde3bb500741d200526e47e6df74c6 debuginfo(build-id) = 5a918516330c428b8cb9608013f7081b5f26fbf2 debuginfo(build-id) = 675453eff7de36ac47c1339567cf2ad1d3907b08 debuginfo(build-id) = 81be22237a74dc72d7a5e6534d4819d794ef8b11 debuginfo(build-id) = 88ca5b20524d80307c7ac5da6bdd4de313dacfb5 debuginfo(build-id) = 8d723f1d7831987ea62be84a7555c72abb018764 debuginfo(build-id) = 96fb20107db2bc0a7075017aec2ad2af1ef39d7c debuginfo(build-id) = 9b7701d681dec5c6407b5c574b318b4b7e035e12 debuginfo(build-id) = 9d443a414165e3e5d6b705583a28ccebd7d34032 debuginfo(build-id) = a0a0b72ff739da510a5a2e1ac8751411e6f66f84 debuginfo(build-id) = a1e468c6bc0ccbb131d19dfb8b0797b62c04e676 debuginfo(build-id) = abee8e06ca3d704f8c55df13e824146e0b70aabf debuginfo(build-id) = abf22b76b152c2f61e2c1125b8d6a7b8084ee2f5 debuginfo(build-id) = b18d28dede0917f19870ec05ad3ed31dd99b8fb5 debuginfo(build-id) = b393068d613f07cc95e85aa55e19d6a275ab132b debuginfo(build-id) = b4574da7b53cda176f031faef9764d72dc13a311 debuginfo(build-id) = b5ff0c698549229e11eebc9c470c8d8b489ff814 debuginfo(build-id) = b83655adb8de24cbaeaabbcdcd882ee654f48082 debuginfo(build-id) = dd2594a079a665554a903daae518c6a26f108f92 debuginfo(build-id) = df68a82c2d096517a78172ba0a8d083b5914b54d debuginfo(build-id) = e1dac2d94946f540c0d6a1410f366fa566459d90 debuginfo(build-id) = e1ead6370ef47acf7087d86272abb9d0a139f7e0 debuginfo(build-id) = e88055db3fa21d9f091871a1feec5597366ef479 debuginfo(build-id) = f1d07a67d58163ebee24b0749918ac5de5867de6 debuginfo(build-id) = f9ef8dea0b7f77d777f74c817b05870161621ab6 debuginfo(build-id) = ffbcf6cd6b54d6ec6b2750f49941f8178558d40c
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: bcftools-debugsource(ppc-64) = 1.13-1.fc35
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le
Wrote: /builddir/build/RPMS/bcftools-debugsource-1.13-1.fc35.ppc64le.rpm
Wrote: /builddir/build/RPMS/bcftools-1.13-1.fc35.ppc64le.rpm
Wrote: /builddir/build/RPMS/bcftools-debuginfo-1.13-1.fc35.ppc64le.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.fVXaAR
+ umask 022
+ cd /builddir/build/BUILD
+ cd bcftools-1.13
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/bcftools-1.13-1.fc35.ppc64le
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0