Mock Version: 3.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64le --nodeps /builddir/build/SPECS/samtools.spec'], chrootPath='/var/lib/mock/fedora-rawhide-ppc64le-1672293995.574551/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 0x7fffab3e1990>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.so80o59i:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.so80o59i:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'fed5897bdc3440d3b6d3c36ba3676b9d', '-D', '/var/lib/mock/fedora-rawhide-ppc64le-1672293995.574551/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.so80o59i:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64le --nodeps /builddir/build/SPECS/samtools.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', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1660521600
Wrote: /builddir/build/SRPMS/samtools-1.15.1-1.fc38.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64le --nodeps /builddir/build/SPECS/samtools.spec'], chrootPath='/var/lib/mock/fedora-rawhide-ppc64le-1672293995.574551/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 0x7fffab3e1990>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.so80o59i:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.so80o59i:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'd47f8e91027249bc8471f05e6d04f47c', '-D', '/var/lib/mock/fedora-rawhide-ppc64le-1672293995.574551/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.so80o59i:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64le --nodeps /builddir/build/SPECS/samtools.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', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1660521600
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.VTwyC1
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf samtools-1.15.1
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/samtools-1.15.1.tar.bz2
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd samtools-1.15.1
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ rm -f INSTALL
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.HjULYw
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd samtools-1.15.1
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/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' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
--- ./htslib-1.15.1/configure.backup 2022-04-07 15:42:52.000000000 +0000
+++ ./htslib-1.15.1/configure 2022-12-29 06:10:19.058240512 +0000
@@ -1697,7 +1697,7 @@
#ifdef __cplusplus
extern "C"
#endif
-char $2 ();
+__attribute__ ((used)) char $2 ();
/* The GNU C library defines this for functions which it implements
to always fail with ENOSYS. Some functions are actually named
something starting with __ and the normal name is an alias. */
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.15.1/configure
+ diff -u ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ mv ./htslib-1.15.1/configure.backup ./htslib-1.15.1/configure
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
++ echo --runstatedir=/run
+ ./configure --build=powerpc64le-redhat-linux-gnu --host=powerpc64le-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 --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' --prefix=/usr --with-htslib=system
checking for gawk... gawk
checking for powerpc64le-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 for NcursesW wide-character library... yes
checking for working ncursesw/curses.h... yes
checking for library containing cbreak... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
+ /usr/bin/make -O -j5 V=1 VERBOSE=1
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. -I./lz4 -c -o bam_aux.o bam_aux.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. -I./lz4 -c -o bam.o bam.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. -I./lz4 -c -o bam_index.o bam_index.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. -I./lz4 -c -o bam_cat.o bam_cat.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. -I./lz4 -c -o bam_plbuf.o bam_plbuf.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. -I./lz4 -c -o bam_md.o bam_md.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. -I./lz4 -c -o bam_reheader.o bam_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. -I./lz4 -c -o bam_fastq.o bam_fastq.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. -I./lz4 -c -o bam_plcmd.o bam_plcmd.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. -I./lz4 -c -o sam_view.o sam_view.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. -I./lz4 -c -o bam_rmdupse.o bam_rmdupse.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. -I./lz4 -c -o bam_color.o bam_color.c
echo '#define SAMTOOLS_VERSION "1.15.1"' > version.h
echo '#define SAMTOOLS_CC "gcc"' >> version.h
echo '#define SAMTOOLS_CPPFLAGS ""' >> version.h
echo '#define SAMTOOLS_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"' >> version.h
echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes"' >> version.h
echo '#define SAMTOOLS_HTSDIR ""' >> version.h
echo '#define SAMTOOLS_LIBS ""' >> version.h
echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> 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. -I./lz4 -c -o bam_rmdup.o bam_rmdup.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. -I./lz4 -c -o bam_stat.o bam_stat.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. -I./lz4 -c -o bam2bcf.o bam2bcf.c
bam2bcf.c: In function 'bcf_call_glfgen':
bam2bcf.c:81:33: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
81 | bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/kstring.h:30,
from /usr/include/htslib/hts.h:37,
from bam2bcf.c:30:
/usr/include/stdlib.h:564:14: note: in a call to allocation function 'realloc' declared here
564 | extern void *realloc (void *__ptr, size_t __size)
| ^~~~~~~
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. -I./lz4 -c -o bam_mate.o bam_mate.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. -I./lz4 -c -o cut_target.o cut_target.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. -I./lz4 -c -o sample.o 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. -I./lz4 -c -o coverage.o coverage.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. -I./lz4 -c -o padding.o padding.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. -I./lz4 -c -o bedcov.o bedcov.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. -I./lz4 -c -o bam2depth.o bam2depth.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. -I./lz4 -c -o faidx.o faidx.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. -I./lz4 -c -o phase.o phase.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. -I./lz4 -c -o dict.o dict.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. -I./lz4 -c -o bam_flags.o bam_flags.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. -I./lz4 -c -o stats_isize.o stats_isize.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. -I./lz4 -c -o bamshuf.o bamshuf.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. -I./lz4 -c -o bam_split.o bam_split.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. -I./lz4 -c -o bam_tview.o bam_tview.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. -I./lz4 -c -o bam_tview_curses.o bam_tview_curses.c
bam_tview_curses.c: In function 'tv_win_help':
bam_tview_curses.c:333:14: warning: 'base' is used uninitialized [-Wuninitialized]
333 | tview_t* base=(tview_t*)base;
| ^~~~
bam_tview_curses.c:333:14: note: 'base' was declared here
333 | tview_t* base=(tview_t*)base;
| ^~~~
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. -I./lz4 -c -o bam_tview_html.o bam_tview_html.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. -I./lz4 -c -o bam_quickcheck.o bam_quickcheck.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. -I./lz4 -c -o bam_lpileup.o bam_lpileup.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. -I./lz4 -c -o bam_addrprg.o bam_addrprg.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. -I./lz4 -c -o tmp_file.o tmp_file.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. -I./lz4 -c -o bam_sort.o bam_sort.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. -I./lz4 -c -o bam_import.o bam_import.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. -I./lz4 -c -o stats.o 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. -I./lz4 -c -o bam_ampliconclip.o bam_ampliconclip.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. -I./lz4 -c -o bam_samples.o bam_samples.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. -I./lz4 -c -o consensus_pileup.o consensus_pileup.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. -I./lz4 -c -o sam_opts.o sam_opts.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. -I./lz4 -c -o sam_utils.o sam_utils.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. -I./lz4 -c -o bam_consensus.o bam_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. -I./lz4 -c -o bam_markdup.o bam_markdup.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. -I./lz4 -c -o amplicon_stats.o amplicon_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 -DMAQ_LONGREADS -I. -I./lz4 -c -o misc/maq2sam-long.o misc/maq2sam.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. -I./lz4 -c -o misc/maq2sam-short.o misc/maq2sam.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. -I./lz4 -c -o misc/md5sum-lite.o misc/md5sum-lite.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. -I./lz4 -c -o misc/md5fa.o misc/md5fa.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. -I./lz4 -c -o bedidx.o bedidx.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. -I./lz4 -c -o misc/ace2sam.o misc/ace2sam.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. -I./lz4 -c -o test/test.o test/test.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. -I./lz4 -c -o misc/wgsim.o misc/wgsim.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. -I./lz4 -c -o test/split/test_count_rg.o test/split/test_count_rg.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. -I./lz4 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.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. -I./lz4 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.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. -I./lz4 -c -o lz4/lz4.o lz4/lz4.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. -I./lz4 -c -o test/vcf-miniview.o test/vcf-miniview.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. -I./lz4 -c -o bamtk.o bamtk.c
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o
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. -I./lz4 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/maq2sam-long misc/maq2sam-long.o -lz
gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/maq2sam-short misc/maq2sam-short.o -lz
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/ace2sam misc/ace2sam.o -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/md5fa misc/md5fa.o -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o misc/wgsim misc/wgsim.o -lm -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread
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. -I./lz4 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread
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. -I./lz4 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread
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. -I./lz4 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -o samtools bam.o bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o ./lz4/lz4.o libst.a -lhts -lncursesw -lm -lz -lpthread
In function 'bcf_call_glfgen',
inlined from 'tv_pl_func' at bam_tview.c:196:9:
bam2bcf.c:81:33: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
81 | bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
| ^
/usr/include/stdlib.h: In function 'tv_pl_func':
/usr/include/stdlib.h:564:14: note: in a call to allocation function 'realloc' declared here
564 | extern void *realloc (void *__ptr, size_t __size)
| ^
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.iY5jHo
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le
++ dirname /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le
+ 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
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd samtools-1.15.1
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/share/man/man1
/usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin
/usr/bin/install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin
/usr/bin/install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin
/usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/share/man/man1
++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/zoom2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/blast2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/bowtie2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/export2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/fasta-sanitize.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/interpolate_sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/novo2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/plot-ampliconstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/plot-bamstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/psl2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/sam2vcf.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/samtools.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/seq_cache_populate.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/soap2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/wgsim_eval.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/zoom2sam.pl
+ /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 1.15.1-1.fc38 --unique-debug-suffix -1.15.1-1.fc38.ppc64le --unique-debug-src-base samtools-1.15.1-1.fc38.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.15.1
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/ace2sam
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/md5fa
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/md5sum-lite
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/maq2sam-long
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/maq2sam-short
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/samtools
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/bin/wgsim
original debug info size: 2432kB, size after compression: 2240kB
/usr/bin/sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match.
2442 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.w6RPgK
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd samtools-1.15.1
+ ldd samtools
+ grep -E '/lib(64)?/libhts\.so\.'
libhts.so.3 => /lib64/libhts.so.3 (0x00007fff81e40000)
+ make test
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
test/split/test_parse_args
REF_PATH=: test/test.pl --exec bgzip= ${TEST_OPTS:-}
bgzip -c -b 65272 -s 5 /tmp/r5Evz6CSKz/bgzip.dat.gz
.. ok
bgzip -c -b 979200 -s 6 /tmp/r5Evz6CSKz/bgzip.dat.gz
.. ok
bgzip -c -b 652804 -s 6 /tmp/r5Evz6CSKz/bgzip.dat.gz
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/r5Evz6CSKz/faidx.fa 3:11-13 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/r5Evz6CSKz/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/r5Evz6CSKz/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/r5Evz6CSKz/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/r5Evz6CSKz/faidx.fa 1:100-104 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/r5Evz6CSKz/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/r5Evz6CSKz/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/r5Evz6CSKz/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/r5Evz6CSKz/fqidx.fq 3:11-13
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/r5Evz6CSKz/fqidx.fq.gz 3:11-13
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/r5Evz6CSKz/fqidx.fq 2:998-1003
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/r5Evz6CSKz/fqidx.fq.gz 2:998-1003
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/r5Evz6CSKz/fqidx.fq 1:100-104
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/r5Evz6CSKz/fqidx.fq.gz 1:100-104
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/r5Evz6CSKz/fqidx.fq 1:99998-100007
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/r5Evz6CSKz/fqidx.fq.gz 1:99998-100007
.. ok
.. ok
test_dict:
/builddir/build/BUILD/samtools-1.15.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /builddir/build/BUILD/samtools-1.15.1/test/dat/dict.fa
.. ok
test_dict:
/builddir/build/BUILD/samtools-1.15.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/r5Evz6CSKz/dict.fa.gz
.. ok
test_dict:
cat /builddir/build/BUILD/samtools-1.15.1/test/dat/dict.fa | /builddir/build/BUILD/samtools-1.15.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz
.. ok
test_dict:
/builddir/build/BUILD/samtools-1.15.1/samtools dict -AH < /builddir/build/BUILD/samtools-1.15.1/test/dat/dict.alias.fa
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools view /tmp/r5Evz6CSKz/large_chrom.bam ref2
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools view /tmp/r5Evz6CSKz/large_chrom.bam ref2:1-541556283
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools index /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools view -X /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /tmp/r5Evz6CSKz/test_input_1_b.bam.bai ref2
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai /tmp/r5Evz6CSKz/test_input_1_b.bam.bai
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools index -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.bam /tmp/r5Evz6CSKz/auto_indexed.csi && cat /tmp/r5Evz6CSKz/auto_indexed.csi
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools index /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.cram /tmp/r5Evz6CSKz/auto_indexed.crai && cat /tmp/r5Evz6CSKz/auto_indexed.crai
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools index -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.sam /tmp/r5Evz6CSKz/auto_indexed.csi && cat /tmp/r5Evz6CSKz/auto_indexed.csi
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/r5Evz6CSKz/large_chrom.bam ref2
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/r5Evz6CSKz/large_chrom.bam ref2:1-541556283
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /tmp/r5Evz6CSKz/test_input_1_b.bam.bai ref2
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam.bai /tmp/r5Evz6CSKz/test_input_1_b.bam.bai
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.bam /tmp/r5Evz6CSKz/auto_indexed.csi && cat /tmp/r5Evz6CSKz/auto_indexed.csi
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.cram /tmp/r5Evz6CSKz/auto_indexed.crai && cat /tmp/r5Evz6CSKz/auto_indexed.crai
.. ok
test_index:
/builddir/build/BUILD/samtools-1.15.1/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.15.1/test/dat/auto_indexed.tmp.sam /tmp/r5Evz6CSKz/auto_indexed.csi && cat /tmp/r5Evz6CSKz/auto_indexed.csi
.. ok
test_mpileup:
/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/r5Evz6CSKz/mpileup.bam.list -f /tmp/r5Evz6CSKz/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/r5Evz6CSKz/mpileup.cram.list -f /tmp/r5Evz6CSKz/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/r5Evz6CSKz/mpileup.bam.urllist -f /tmp/r5Evz6CSKz/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/r5Evz6CSKz/mpileup.cram.urllist -f /tmp/r5Evz6CSKz/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/r5Evz6CSKz/mpileup.ref.fa.gz -r17:1050-1060 /tmp/r5Evz6CSKz/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/r5Evz6CSKz/mpileup.ref.fa.gz -r17:1050-1060 /tmp/r5Evz6CSKz/mpileup.1.cram | grep -v mpileup
.. ok
test_mpileup:
/builddir/build/BUILD/samtools-1.15.1/samtools mpileup /builddir/build/BUILD/samtools-1.15.1/test/mpileup/overlap.bam | grep 128814202
test/test.pl: no IO::Pty module or can't open pty; skipping usage tests
.. ok
test_usage:
samtools
test_view:
Generating test data file .................. done
1: SAM -> BAM -> SAM .. ok
2: SAM -> uncompressed BAM .. ok
3: uncompressed BAM -> SAM and compare .. ok
4: SAM -> fast compressed BAM .. ok
5: fast compressed BAM -> SAM and compare .. ok
6: SAM -> CRAM -> SAM (UR header tags) .. ok
7: SAM -> CRAM -> SAM (M5 header tags) .. ok
8: BAM -> CRAM with UR -> SAM .. ok
9: SAM -> BAM (M5 header tags) .. ok
10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok
11: CRAM -> BAM with UR .. ok
12: CRAM -> BAM with M5 .. ok
13: SAM -> SAM via stdout .. ok
14: SAM -> BAM via stdout .. ok
15: SAM -> CRAM via stdout .. ok
16: SAM from stdin -> SAM .. ok
17: BAM from stdin -> SAM .. ok
18: CRAM from stdin -> SAM .. ok
19: samtools view -H (SAM input) .. ok
20: samtools view -H (BAM input) .. ok
21: samtools view -H (CRAM input) .. ok
22: No headers (SAM input) .. ok
23: No headers (BAM input) .. ok
24: No headers (CRAM input) .. ok
25: Filter -f 128 (SAM input) .. ok
26: Count -f 128 (SAM input) .. ok
27: Filter -f 128 (BAM input) .. ok
28: Count -f 128 (BAM input) .. ok
29: Filter -f 128 (CRAM input) .. ok
30: Count -f 128 (CRAM input) .. ok
31: Filter -F 128 (SAM input) .. ok
32: Count -F 128 (SAM input) .. ok
33: Filter -F 128 (BAM input) .. ok
34: Count -F 128 (BAM input) .. ok
35: Filter -F 128 (CRAM input) .. ok
36: Count -F 128 (CRAM input) .. ok
37: Filter -F 128 -f 2 (SAM input) .. ok
38: Count -F 128 -f 2 (SAM input) .. ok
39: Filter -F 128 -f 2 (BAM input) .. ok
40: Count -F 128 -f 2 (BAM input) .. ok
41: Filter -F 128 -f 2 (CRAM input) .. ok
42: Count -F 128 -f 2 (CRAM input) .. ok
43: Filter -r grp2 (SAM input) .. ok
44: Count -r grp2 (SAM input) .. ok
45: Filter -r grp2 (BAM input) .. ok
46: Count -r grp2 (BAM input) .. ok
47: Filter -r grp2 (CRAM input) .. ok
48: Count -r grp2 (CRAM input) .. ok
49: Filter -R /tmp/r5Evz6CSKz/view.001.fogn (SAM input) .. ok
50: Count -R /tmp/r5Evz6CSKz/view.001.fogn (SAM input) .. ok
51: Filter -R /tmp/r5Evz6CSKz/view.001.fogn (BAM input) .. ok
52: Count -R /tmp/r5Evz6CSKz/view.001.fogn (BAM input) .. ok
53: Filter -R /tmp/r5Evz6CSKz/view.001.fogn (CRAM input) .. ok
54: Count -R /tmp/r5Evz6CSKz/view.001.fogn (CRAM input) .. ok
55: Filter -R /tmp/r5Evz6CSKz/view.001.fogn -r grp2 (SAM input).. ok
56: Count -R /tmp/r5Evz6CSKz/view.001.fogn -r grp2 (SAM input).. ok
57: Filter -R /tmp/r5Evz6CSKz/view.001.fogn -r grp2 (BAM input).. ok
58: Count -R /tmp/r5Evz6CSKz/view.001.fogn -r grp2 (BAM input).. ok
59: Filter -R /tmp/r5Evz6CSKz/view.001.fogn -r grp2 (CRAM input).. ok
60: Count -R /tmp/r5Evz6CSKz/view.001.fogn -r grp2 (CRAM input).. ok
61: Filter -r grp2 -R /tmp/r5Evz6CSKz/view.001.fogn (SAM input).. ok
62: Count -r grp2 -R /tmp/r5Evz6CSKz/view.001.fogn (SAM input).. ok
63: Filter -r grp2 -R /tmp/r5Evz6CSKz/view.001.fogn (BAM input).. ok
64: Count -r grp2 -R /tmp/r5Evz6CSKz/view.001.fogn (BAM input).. ok
65: Filter -r grp2 -R /tmp/r5Evz6CSKz/view.001.fogn (CRAM input).. ok
66: Count -r grp2 -R /tmp/r5Evz6CSKz/view.001.fogn (CRAM input).. ok
67: Filter -N /tmp/r5Evz6CSKz/view.001.forn (SAM input) .. ok
68: Count -N /tmp/r5Evz6CSKz/view.001.forn (SAM input) .. ok
69: Filter -N /tmp/r5Evz6CSKz/view.001.forn (BAM input) .. ok
70: Count -N /tmp/r5Evz6CSKz/view.001.forn (BAM input) .. ok
71: Filter -N /tmp/r5Evz6CSKz/view.001.forn (CRAM input) .. ok
72: Count -N /tmp/r5Evz6CSKz/view.001.forn (CRAM input) .. ok
73: Filter -d BC (SAM input) .. ok
74: Count -d BC (SAM input) .. ok
75: Filter -d BC (BAM input) .. ok
76: Count -d BC (BAM input) .. ok
77: Filter -d BC (CRAM input) .. ok
78: Count -d BC (CRAM input) .. ok
79: Filter -d BC:TGCA (SAM input) .. ok
80: Count -d BC:TGCA (SAM input) .. ok
81: Filter -d BC:TGCA (BAM input) .. ok
82: Count -d BC:TGCA (BAM input) .. ok
83: Filter -d BC:TGCA (CRAM input) .. ok
84: Count -d BC:TGCA (CRAM input) .. ok
85: Filter -D BC:/tmp/r5Evz6CSKz/view.001.fobc (SAM input) .. ok
86: Count -D BC:/tmp/r5Evz6CSKz/view.001.fobc (SAM input) .. ok
87: Filter -D BC:/tmp/r5Evz6CSKz/view.001.fobc (BAM input) .. ok
88: Count -D BC:/tmp/r5Evz6CSKz/view.001.fobc (BAM input) .. ok
89: Filter -D BC:/tmp/r5Evz6CSKz/view.001.fobc (CRAM input) .. ok
90: Count -D BC:/tmp/r5Evz6CSKz/view.001.fobc (CRAM input) .. ok
91: Filter -D BC:/tmp/r5Evz6CSKz/view.001.fobc -d BC:TGCA (SAM input).. ok
92: Count -D BC:/tmp/r5Evz6CSKz/view.001.fobc -d BC:TGCA (SAM input).. ok
93: Filter -D BC:/tmp/r5Evz6CSKz/view.001.fobc -d BC:TGCA (BAM input).. ok
94: Count -D BC:/tmp/r5Evz6CSKz/view.001.fobc -d BC:TGCA (BAM input).. ok
95: Filter -D BC:/tmp/r5Evz6CSKz/view.001.fobc -d BC:TGCA (CRAM input).. ok
96: Count -D BC:/tmp/r5Evz6CSKz/view.001.fobc -d BC:TGCA (CRAM input).. ok
97: Filter -d BC:TGCA -D BC:/tmp/r5Evz6CSKz/view.001.fobc (SAM input).. ok
98: Count -d BC:TGCA -D BC:/tmp/r5Evz6CSKz/view.001.fobc (SAM input).. ok
99: Filter -d BC:TGCA -D BC:/tmp/r5Evz6CSKz/view.001.fobc (BAM input).. ok
100: Count -d BC:TGCA -D BC:/tmp/r5Evz6CSKz/view.001.fobc (BAM input).. ok
101: Filter -d BC:TGCA -D BC:/tmp/r5Evz6CSKz/view.001.fobc (CRAM input).. ok
102: Count -d BC:TGCA -D BC:/tmp/r5Evz6CSKz/view.001.fobc (CRAM input).. ok
103: Filter -D RG:/tmp/r5Evz6CSKz/view.001.fogn (SAM input) .. ok
104: Count -D RG:/tmp/r5Evz6CSKz/view.001.fogn (SAM input) .. ok
105: Filter -D RG:/tmp/r5Evz6CSKz/view.001.fogn (BAM input) .. ok
106: Count -D RG:/tmp/r5Evz6CSKz/view.001.fogn (BAM input) .. ok
107: Filter -D RG:/tmp/r5Evz6CSKz/view.001.fogn (CRAM input).. ok
108: Count -D RG:/tmp/r5Evz6CSKz/view.001.fogn (CRAM input) .. ok
109: Filter -d NE:TGCA (SAM input) .. ok
110: Count -d NE:TGCA (SAM input) .. ok
111: Filter -d NE:TGCA (BAM input) .. ok
112: Count -d NE:TGCA (BAM input) .. ok
113: Filter -d NE:TGCA (CRAM input) .. ok
114: Count -d NE:TGCA (CRAM input) .. ok
115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/r5Evz6CSKz/view.test115.sam -h -d TGCA /tmp/r5Evz6CSKz/view.001.sam --no-PG
.. expected failure
116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -c -d TGCA /tmp/r5Evz6CSKz/view.001.sam --no-PG
.. expected failure
117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/r5Evz6CSKz/view.test117.sam -h -d TGCA /tmp/r5Evz6CSKz/view.test001.bam --no-PG
.. expected failure
118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -c -d TGCA /tmp/r5Evz6CSKz/view.test001.bam --no-PG
.. expected failure
119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/r5Evz6CSKz/view.test119.sam -h -d TGCA /tmp/r5Evz6CSKz/view.test006.cram --no-PG
.. expected failure
120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -c -d TGCA /tmp/r5Evz6CSKz/view.test006.cram --no-PG
.. expected failure
121: Filter -D BClong:/tmp/r5Evz6CSKz/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/r5Evz6CSKz/view.001.fobc"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/r5Evz6CSKz/view.test121.sam -h -D BClong:/tmp/r5Evz6CSKz/view.001.fobc /tmp/r5Evz6CSKz/view.001.sam --no-PG
.. expected failure
122: Count -D BClong:/tmp/r5Evz6CSKz/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/r5Evz6CSKz/view.001.fobc"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/r5Evz6CSKz/view.001.fobc /tmp/r5Evz6CSKz/view.001.sam --no-PG
.. expected failure
123: Filter -D BClong:/tmp/r5Evz6CSKz/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/r5Evz6CSKz/view.001.fobc"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/r5Evz6CSKz/view.test123.sam -h -D BClong:/tmp/r5Evz6CSKz/view.001.fobc /tmp/r5Evz6CSKz/view.test001.bam --no-PG
.. expected failure
124: Count -D BClong:/tmp/r5Evz6CSKz/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/r5Evz6CSKz/view.001.fobc"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/r5Evz6CSKz/view.001.fobc /tmp/r5Evz6CSKz/view.test001.bam --no-PG
.. expected failure
125: Filter -D BClong:/tmp/r5Evz6CSKz/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/r5Evz6CSKz/view.001.fobc"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/r5Evz6CSKz/view.test125.sam -h -D BClong:/tmp/r5Evz6CSKz/view.001.fobc /tmp/r5Evz6CSKz/view.test006.cram --no-PG
.. expected failure
126: Count -D BClong:/tmp/r5Evz6CSKz/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/r5Evz6CSKz/view.001.fobc"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/r5Evz6CSKz/view.001.fobc /tmp/r5Evz6CSKz/view.test006.cram --no-PG
.. expected failure
127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/r5Evz6CSKz/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/r5Evz6CSKz/view.001.sam --no-PG
.. expected failure
128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/r5Evz6CSKz/view.001.sam --no-PG
.. expected failure
129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/r5Evz6CSKz/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/r5Evz6CSKz/view.test001.bam --no-PG
.. expected failure
130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/r5Evz6CSKz/view.test001.bam --no-PG
.. expected failure
131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/r5Evz6CSKz/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/r5Evz6CSKz/view.test006.cram --no-PG
.. expected failure
132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
/builddir/build/BUILD/samtools-1.15.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/r5Evz6CSKz/view.test006.cram --no-PG
.. expected failure
133: Filter -d NM:13 (SAM input) .. ok
134: Count -d NM:13 (SAM input) .. ok
135: Filter -d NM:13 (BAM input) .. ok
136: Count -d NM:13 (BAM input) .. ok
137: Filter -d NM:13 (CRAM input) .. ok
138: Count -d NM:13 (CRAM input) .. ok
139: Filter -d ab:z (SAM input) .. ok
140: Count -d ab:z (SAM input) .. ok
141: Filter -d ab:z (BAM input) .. ok
142: Count -d ab:z (BAM input) .. ok
143: Filter -d ab:z (CRAM input) .. ok
144: Count -d ab:z (CRAM input) .. ok
145: Filter -l Library 2 (SAM input) .. ok
146: Count -l Library 2 (SAM input) .. ok
147: Filter -l Library 2 (BAM input) .. ok
148: Count -l Library 2 (BAM input) .. ok
149: Filter -l Library 2 (CRAM input) .. ok
150: Count -l Library 2 (CRAM input) .. ok
151: Filter -l Library 3 (SAM input) .. ok
152: Count -l Library 3 (SAM input) .. ok
153: Filter -l Library 3 (BAM input) .. ok
154: Count -l Library 3 (BAM input) .. ok
155: Filter -l Library 3 (CRAM input) .. ok
156: Count -l Library 3 (CRAM input) .. ok
157: Filter -q 50 (SAM input) .. ok
158: Count -q 50 (SAM input) .. ok
159: Filter -q 50 (BAM input) .. ok
160: Count -q 50 (BAM input) .. ok
161: Filter -q 50 (CRAM input) .. ok
162: Count -q 50 (CRAM input) .. ok
163: Filter -q 99 (SAM input) .. ok
164: Count -q 99 (SAM input) .. ok
165: Filter -q 99 (BAM input) .. ok
166: Count -q 99 (BAM input) .. ok
167: Filter -q 99 (CRAM input) .. ok
168: Count -q 99 (CRAM input) .. ok
169: Filter -q 100 (SAM input) .. ok
170: Count -q 100 (SAM input) .. ok
171: Filter -q 100 (BAM input) .. ok
172: Count -q 100 (BAM input) .. ok
173: Filter -q 100 (CRAM input) .. ok
174: Count -q 100 (CRAM input) .. ok
175: Filter -x fa (SAM input) .. ok
176: Count -x fa (SAM input) .. ok
177: Filter -x fa (BAM input) .. ok
178: Count -x fa (BAM input) .. ok
179: Filter -x fa (CRAM input) .. ok
180: Count -x fa (CRAM input) .. ok
181: Filter -x fa -x ha (SAM input) .. ok
182: Count -x fa -x ha (SAM input) .. ok
183: Filter -x fa -x ha (BAM input) .. ok
184: Count -x fa -x ha (BAM input) .. ok
185: Filter -x fa -x ha (CRAM input) .. ok
186: Count -x fa -x ha (CRAM input) .. ok
187: Filter -x fa,ha (SAM input) .. ok
188: Count -x fa,ha (SAM input) .. ok
189: Filter -x fa,ha (BAM input) .. ok
190: Count -x fa,ha (BAM input) .. ok
191: Filter -x fa,ha (CRAM input) .. ok
192: Count -x fa,ha (CRAM input) .. ok
193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok
194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok
195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok
196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok
197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok
198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok
199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok
200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok
201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok
202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok
203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok
204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok
205: Filter -x fa -r grp2 (SAM input) .. ok
206: Count -x fa -r grp2 (SAM input) .. ok
207: Filter -x fa -r grp2 (BAM input) .. ok
208: Count -x fa -r grp2 (BAM input) .. ok
209: Filter -x fa -r grp2 (CRAM input) .. ok
210: Count -x fa -r grp2 (CRAM input) .. ok
211: Filter -x RG -r grp2 (SAM input) .. ok
212: Count -x RG -r grp2 (SAM input) .. ok
213: Filter -x RG -r grp2 (BAM input) .. ok
214: Count -x RG -r grp2 (BAM input) .. ok
215: Filter -x RG -r grp2 (CRAM input) .. ok
216: Count -x RG -r grp2 (CRAM input) .. ok
217: Filter -m 10 (SAM input) .. ok
218: Count -m 10 (SAM input) .. ok
219: Filter -m 10 (BAM input) .. ok
220: Count -m 10 (BAM input) .. ok
221: Filter -m 10 (CRAM input) .. ok
222: Count -m 10 (CRAM input) .. ok
223: Filter -m 11 (SAM input) .. ok
224: Count -m 11 (SAM input) .. ok
225: Filter -m 11 (BAM input) .. ok
226: Count -m 11 (BAM input) .. ok
227: Filter -m 11 (CRAM input) .. ok
228: Count -m 11 (CRAM input) .. ok
229: Filter -m 15 (SAM input) .. ok
230: Count -m 15 (SAM input) .. ok
231: Filter -m 15 (BAM input) .. ok
232: Count -m 15 (BAM input) .. ok
233: Filter -m 15 (CRAM input) .. ok
234: Count -m 15 (CRAM input) .. ok
235: Filter -m 16 (SAM input) .. ok
236: Count -m 16 (SAM input) .. ok
237: Filter -m 16 (BAM input) .. ok
238: Count -m 16 (BAM input) .. ok
239: Filter -m 16 (CRAM input) .. ok
240: Count -m 16 (CRAM input) .. ok
241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok
242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok
243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok
244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok
245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok
246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok
247: Filter -e [BC] (SAM input) .. ok
248: Count -e [BC] (SAM input) .. ok
249: Filter -e [BC] (BAM input) .. ok
250: Count -e [BC] (BAM input) .. ok
251: Filter -e [BC] (CRAM input) .. ok
252: Count -e [BC] (CRAM input) .. ok
253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok
254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok
255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok
256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok
257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok
258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok
259: Filter -e mapq >= 50 (SAM input) .. ok
260: Count -e mapq >= 50 (SAM input) .. ok
261: Filter -e mapq >= 50 (BAM input) .. ok
262: Count -e mapq >= 50 (BAM input) .. ok
263: Filter -e mapq >= 50 (CRAM input) .. ok
264: Count -e mapq >= 50 (CRAM input) .. ok
265: Filter -e mapq >= 99 (SAM input) .. ok
266: Count -e mapq >= 99 (SAM input) .. ok
267: Filter -e mapq >= 99 (BAM input) .. ok
268: Count -e mapq >= 99 (BAM input) .. ok
269: Filter -e mapq >= 99 (CRAM input) .. ok
270: Count -e mapq >= 99 (CRAM input) .. ok
271: Filter -e mapq >= 100 (SAM input) .. ok
272: Count -e mapq >= 100 (SAM input) .. ok
273: Filter -e mapq >= 100 (BAM input) .. ok
274: Count -e mapq >= 100 (BAM input) .. ok
275: Filter -e mapq >= 100 (CRAM input) .. ok
276: Count -e mapq >= 100 (CRAM input) .. ok
277: 1bp reads file SAM -> BAM -> SAM .. ok
278: 1bp reads file SAM -> CRAM -> SAM .. ok
278: Region Z (BAM input) .. ok
279: Count Z (BAM input) .. ok
280: Region Z (CRAM input) .. ok
281: Count Z (CRAM input) .. ok
282: Region Z:30 (BAM input) .. ok
283: Count Z:30 (BAM input) .. ok
284: Region Z:30 (CRAM input) .. ok
285: Count Z:30 (CRAM input) .. ok
286: Region Z:20-40 (BAM input) .. ok
287: Count Z:20-40 (BAM input) .. ok
288: Region Z:20-40 (CRAM input) .. ok
289: Count Z:20-40 (CRAM input) .. ok
290: Region ref1 (BAM input) .. ok
291: Count ref1 (BAM input) .. ok
292: Region ref1 (CRAM input) .. ok
293: Count ref1 (CRAM input) .. ok
294: Region ref1:15 (BAM input) .. ok
295: Count ref1:15 (BAM input) .. ok
296: Region ref1:15 (CRAM input) .. ok
297: Count ref1:15 (CRAM input) .. ok
298: Region ref1:15-45 (BAM input) .. ok
299: Count ref1:15-45 (BAM input) .. ok
300: Region ref1:15-45 (CRAM input) .. ok
301: Count ref1:15-45 (CRAM input) .. ok
302: Region ref1:15-45 ref2 (BAM input) .. ok
303: Count ref1:15-45 ref2 (BAM input) .. ok
304: Region ref1:15-45 ref2 (CRAM input) .. ok
305: Count ref1:15-45 ref2 (CRAM input) .. ok
306: Region ref1:15-45 ref2:16 (BAM input) .. ok
307: Count ref1:15-45 ref2:16 (BAM input) .. ok
308: Region ref1:15-45 ref2:16 (CRAM input) .. ok
309: Count ref1:15-45 ref2:16 (CRAM input) .. ok
310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
318: Region -f 128 ref1 (BAM input) .. ok
319: Count -f 128 ref1 (BAM input) .. ok
320: Region -f 128 ref1 (CRAM input) .. ok
321: Count -f 128 ref1 (CRAM input) .. ok
322: Region -q 50 ref1:15-45 (BAM input) .. ok
323: Count -q 50 ref1:15-45 (BAM input) .. ok
324: Region -q 50 ref1:15-45 (CRAM input) .. ok
325: Count -q 50 ref1:15-45 (CRAM input) .. ok
326: Region -r grp2 ref1:15-45 (BAM input) .. ok
327: Count -r grp2 ref1:15-45 (BAM input) .. ok
328: Region -r grp2 ref1:15-45 (CRAM input) .. ok
329: Count -r grp2 ref1:15-45 (CRAM input) .. ok
330: Region * (BAM input) .. ok
331: Count * (BAM input) .. ok
332: Region * (CRAM input) .. ok
333: Count * (CRAM input) .. ok
334: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed (BAM input).. ok
335: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed (BAM input).. ok
336: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed (CRAM input).. ok
337: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed (CRAM input).. ok
338: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.02.bed (BAM input).. ok
339: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.02.bed (BAM input).. ok
340: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.02.bed (CRAM input).. ok
341: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.02.bed (CRAM input).. ok
342: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed (BAM input).. ok
343: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed (BAM input).. ok
344: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed (CRAM input).. ok
345: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed (CRAM input).. ok
346: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.02.bed (BAM input).. ok
347: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.02.bed (BAM input).. ok
348: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.02.bed (CRAM input).. ok
349: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.02.bed (CRAM input).. ok
350: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z (BAM input).. ok
351: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z (BAM input).. ok
352: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z (CRAM input).. ok
353: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z (CRAM input).. ok
354: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok
355: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok
356: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
357: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
358: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
359: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
360: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
361: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
362: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
363: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
364: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
365: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
366: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
367: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
368: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
369: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
370: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (BAM input).. ok
371: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (BAM input).. ok
372: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok
373: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok
374: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
375: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
376: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
377: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
378: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
379: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
380: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
381: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
382: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok
383: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok
384: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
385: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
386: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok
387: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok
388: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
389: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
390: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
391: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
392: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
393: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
394: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok
395: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok
396: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok
397: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok
398: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok
399: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok
400: Region -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok
401: Count -L /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok
402: Make BAM with no M5/UR tags .. ok
403: Add @SQ with -t (SAM -> SAM) .. ok
404: Add @SQ with -T (SAM -> SAM) .. ok
405: Add @SQ with -t (BAM -> SAM) .. ok
406: Add @SQ with -T (BAM -> SAM) .. ok
407: Add @SQ with -t (SAM -> BAM) .. ok
408: Add @SQ with -T (SAM -> BAM) .. ok
409: Add @SQ with -t (BAM -> BAM) .. ok
410: Add @SQ with -T (BAM -> BAM) .. ok
411: Add @SQ with -t (SAM -> CRAM) .. ok
412: Add @SQ with -T (SAM -> CRAM) .. ok
413: Add @SQ with -t (BAM -> CRAM) .. ok
414: Add @SQ with -T (BAM -> CRAM) .. ok
415: Make CRAM with no UR field .. ok
416: Decoding CRAM with no UR field via -T .. ok
417: CIGAR B-operator removal .. ok
418: Big SAM -> BAM .. ok
419: Big SAM -> BAM (2 threads) .. ok
420: Big SAM -> BAM (4 threads) .. ok
421: Big SAM -> CRAM .. ok
422: Big SAM -> CRAM (2 threads) .. ok
423: Big SAM -> CRAM (4 threads) .. ok
424: Subsample 0.2 (SAM input) ............ ok
425: Subsample 0.5 (SAM input) ............ ok
426: Subsample 0.8 (SAM input) ............ ok
427: Subsample 0.2 (BAM input) ............ ok
428: Subsample 0.5 (BAM input) ............ ok
429: Subsample 0.8 (BAM input) ............ ok
430: Subsample 0.2 (CRAM input) ............ ok
431: Subsample 0.5 (CRAM input) ............ ok
432: Subsample 0.8 (CRAM input) ............ ok
433: SAM add PG .. ok
434: Unset dup flag, remove dt and do tags .. ok
435: Unmap dup flagged reads. .. ok
436: Unmap dup flagged reads. .. ok
437: fetch pairs .. ok
438: fetch pairs .. ok
439: fetch pairs .. ok
test_head:
/builddir/build/BUILD/samtools-1.15.1/samtools head /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam
.. ok
test_head:
/builddir/build/BUILD/samtools-1.15.1/samtools head -h 0 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam
.. ok
test_head:
/builddir/build/BUILD/samtools-1.15.1/samtools head -h 1 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam
.. ok
test_head:
/builddir/build/BUILD/samtools-1.15.1/samtools head -h 5 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam
.. ok
test_head:
/builddir/build/BUILD/samtools-1.15.1/samtools head -h 29 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam
.. ok
test_head:
/builddir/build/BUILD/samtools-1.15.1/samtools head -h 30 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam
.. ok
test_head:
/builddir/build/BUILD/samtools-1.15.1/samtools head -n 0 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam
.. ok
test_head:
/builddir/build/BUILD/samtools-1.15.1/samtools head -n 1 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam
.. ok
test_head:
/builddir/build/BUILD/samtools-1.15.1/samtools head -n 5 /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam
.. ok
test_head:
/builddir/build/BUILD/samtools-1.15.1/samtools head -h 5 -n 5 < /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.sam
.. ok
test_cat:
Generating test data file .................. done
Generate BAM file #1 .. ok
Generate CRAM file #1 .. ok
Generating test data file .................. done
Generate BAM file #2 .. ok
Generate CRAM file #2 .. ok
Generating test data file .................. done
Generate BAM file #3 .. ok
Generate CRAM file #3 .. ok
Generating test data file .................. done
Generate BAM file #4 .. ok
Generate CRAM file #4 .. ok
1: cat BAM files .. ok
2: cat recompressed BAM files .. ok
3: cat CRAM files .. ok
4: cat BAM files to stdout .. ok
5: cat recompressed BAM files to stdout .. ok
6: cat CRAM files to stdout .. ok
7: cat BAM files with new header .. ok
8: cat recompressed BAM files with new header .. ok
9: cat CRAM files with new header .. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import -0 test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import -s test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import -s test/bam2fq/5.s.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -T RG,BC,QT -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -T RG,BC,QT,MD,ia -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid'
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import test/import/2.interleaved.fq -T ""
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import test/import/3.interleaved.fq -i
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import test/import/4.aux.fq -T "*"
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import test/import/4.aux.fq -T ""
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import test/import/4.aux.fq -T XZ,XA,AA
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq
.. ok
test_import:
/builddir/build/BUILD/samtools-1.15.1/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ
.. ok
test_bam2fq:
Generate BAM file .. ok
Generate CRAM file .. ok
1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.002.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.003.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.010.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -t -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.703.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.15.1/test/o.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fasta -N -1 /builddir/build/BUILD/samtools-1.15.1/test/o.fa -2 /builddir/build/BUILD/samtools-1.15.1/test/o.fa /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -o /builddir/build/BUILD/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -N -s /tmp/r5Evz6CSKz/bam2fq.discard.s.fq -0 /tmp/r5Evz6CSKz/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.013.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.15.1/test/i2.fq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.014.sam
.. ok
test_bam2fq:
Generate BAM file (2 threads) .. ok
Generate CRAM file (2 threads) .. ok
1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.002.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.003.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.010.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.15.1/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -t -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i.fq -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.15.1/test/s.fq -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.15.1/test/1.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/2.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.703.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -1 /builddir/build/BUILD/samtools-1.15.1/test/o.fq -2 /builddir/build/BUILD/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fasta -@ 2 -N -1 /builddir/build/BUILD/samtools-1.15.1/test/o.fa -2 /builddir/build/BUILD/samtools-1.15.1/test/o.fa /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -o /builddir/build/BUILD/samtools-1.15.1/test/o.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -N -s /tmp/r5Evz6CSKz/bam2fq.discard.s.fq -0 /tmp/r5Evz6CSKz/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.013.sam
.. ok
test_bam2fq:
/builddir/build/BUILD/samtools-1.15.1/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /builddir/build/BUILD/samtools-1.15.1/test/i1.fq --i2 /builddir/build/BUILD/samtools-1.15.1/test/i2.fq -0 /builddir/build/BUILD/samtools-1.15.1/test/0.fq /builddir/build/BUILD/samtools-1.15.1/test/dat/bam2fq.014.sam
.. ok
test_depad:
Generate BAM file .. ok
depad (SAM input) .. ok
depad -s (SAM input) .. ok
depad -u (SAM input) .. ok
depad -1 (SAM input) .. ok
depad (BAM input) .. ok
depad -s (BAM input) .. ok
depad -u (BAM input) .. ok
depad -1 (BAM input) .. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/1_map_cigar_large.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/4_X_cigar_full_seq.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/5_insert_cigar_large.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa -i 0 /builddir/build/BUILD/samtools-1.15.1/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/7_supp.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/7_supp_large.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/8_secondary.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/8_secondary_large.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.15.1/test/stat/test.fa /builddir/build/BUILD/samtools-1.15.1/test/stat/10_map_cigar.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -t /builddir/build/BUILD/samtools-1.15.1/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -g 4 -t /builddir/build/BUILD/samtools-1.15.1/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -g 4 /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.15.1/test/stat/12_3reads.bed | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.15.1/test/stat/12_3reads.bed | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.15.1/test/stat/12_2reads.bed | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.15.1/test/stat/12_2reads.bed | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_ok.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4
/builddir/build/BUILD/samtools-1.15.1/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4
/builddir/build/BUILD/samtools-1.15.1/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats /builddir/build/BUILD/samtools-1.15.1/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4
/builddir/build/BUILD/samtools-1.15.1/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -I s1 /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -I grp2 /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -I grp3 /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam | tail -n+4
.. ok
test_stats:
/builddir/build/BUILD/samtools-1.15.1/samtools stats -I Sample /builddir/build/BUILD/samtools-1.15.1/test/stat/11_target.bam | tail -n+4
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.bam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam -b /tmp/AF_mqbKrE7 - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b_regex.sam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/r5Evz6CSKz/merge.tag.1.bam /tmp/r5Evz6CSKz/merge.tag.2.bam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/r5Evz6CSKz/merge.tag.3.bam /tmp/r5Evz6CSKz/merge.tag.4.bam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge --no-PG -O SAM - /builddir/build/BUILD/samtools-1.15.1/test/merge/test_no_pg_rg_co.sam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.15.1/test/merge/merge.bed - /tmp/r5Evz6CSKz/merge.bed.1.bam /tmp/r5Evz6CSKz/merge.bed.2.bam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.bam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/V_RYNR28mj - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.bam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b_regex.sam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_c.sam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/r5Evz6CSKz/merge.tag.1.bam /tmp/r5Evz6CSKz/merge.tag.2.bam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/r5Evz6CSKz/merge.tag.3.bam /tmp/r5Evz6CSKz/merge.tag.4.bam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 --no-PG -O SAM - /builddir/build/BUILD/samtools-1.15.1/test/merge/test_no_pg_rg_co.sam
.. ok
test_merge:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -@ 2 --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.15.1/test/merge/merge.bed - /tmp/r5Evz6CSKz/merge.bed.1.bam /tmp/r5Evz6CSKz/merge.bed.2.bam
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/r5Evz6CSKz/sortout
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -f /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/r5Evz6CSKz/sortout.bam
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -o /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/r5Evz6CSKz/sorttmp
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -n -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -t AS -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -t FI -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/r5Evz6CSKz/sortout
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -f /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/r5Evz6CSKz/sortout.bam
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -o /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam /tmp/r5Evz6CSKz/sorttmp
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -n -t RG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam -O SAM -o -
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -t AS -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_sort:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -@ 2 -t FI -m 10M /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam -O SAM -o -
.. ok
test_collate:
/builddir/build/BUILD/samtools-1.15.1/samtools collate --output-fmt=sam -O /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam
.. ok
test_collate:
/builddir/build/BUILD/samtools-1.15.1/samtools collate -o /builddir/build/BUILD/samtools-1.15.1/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam
.. ok
test_collate:
/builddir/build/BUILD/samtools-1.15.1/samtools collate -o /builddir/build/BUILD/samtools-1.15.1/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1/test/collate/collate2.tmp
.. ok
test_collate:
/builddir/build/BUILD/samtools-1.15.1/samtools collate --output-fmt=sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1/test/collate/collate3.tmp
.. ok
test_collate:
/builddir/build/BUILD/samtools-1.15.1/samtools collate --output-fmt=sam -f /builddir/build/BUILD/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1/test/collate/1_fast_collate.sam
.. ok
test_collate:
/builddir/build/BUILD/samtools-1.15.1/samtools collate --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1/test/collate/2_fast_collate_with_tmp.sam
.. ok
test_collate:
/builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam -O /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam
.. ok
test_collate:
/builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.15.1/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam
.. ok
test_collate:
/builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.15.1/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1/test/collate/collate2.tmp
.. ok
test_collate:
/builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.15.1/test/collate/collate3.tmp
.. ok
test_collate:
/builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam -f /builddir/build/BUILD/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1/test/collate/1_fast_collate.sam
.. ok
test_collate:
/builddir/build/BUILD/samtools-1.15.1/samtools collate -@ 2 --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.15.1/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.15.1/test/collate/2_fast_collate_with_tmp.sam
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/1_coord_sort.sam -
ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
.. expected failure
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/2_isize_overflow.sam -
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/5_ct.sam -
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/6_ct_replace.sam -
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/7_two_read_mapped.sam -
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/8_isize_overflow_64bit.sam -
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/1_coord_sort.sam -
ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
.. expected failure
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/2_isize_overflow.sam -
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/5_ct.sam -
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/6_ct_replace.sam -
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/7_two_read_mapped.sam -
.. ok
test_fixmate:
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.15.1/test/fixmate/8_isize_overflow_64bit.sam -
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools calmd -uAr /builddir/build/BUILD/samtools-1.15.1/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/mpileup.ref.fa
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools calmd -@ 2 -uAr /builddir/build/BUILD/samtools-1.15.1/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/mpileup.ref.fa
.. ok
test_idxstat:
/builddir/build/BUILD/samtools-1.15.1/samtools idxstats /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.bam
.. ok
test_idxstat:
/builddir/build/BUILD/samtools-1.15.1/samtools idxstats /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.cram
.. ok
test_idxstat:
/builddir/build/BUILD/samtools-1.15.1/samtools idxstats /builddir/build/BUILD/samtools-1.15.1/test/dat/test_input_1_a.sam
.. ok
test_quickcheck:
/builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/1.quickcheck.badeof.bam
.. ok
test_quickcheck:
/builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/2.quickcheck.badheader.bam
.. ok
test_quickcheck:
/builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/3.quickcheck.ok.bam
.. ok
test_quickcheck:
/builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/4.quickcheck.ok.bam
.. ok
test_quickcheck:
/builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram
.. ok
test_quickcheck:
/builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/6.quickcheck.cram21.ok.cram
.. ok
test_quickcheck:
/builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/7.quickcheck.cram30.ok.cram
.. ok
test_quickcheck:
/builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/8.quickcheck.cram21.truncated.cram
.. ok
test_quickcheck:
/builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/9.quickcheck.cram30.truncated.cram
.. ok
test_quickcheck:
/builddir/build/BUILD/samtools-1.15.1/samtools quickcheck /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/10.quickcheck.notargets.bam
.. ok
test_quickcheck:
/builddir/build/BUILD/samtools-1.15.1/samtools quickcheck -v /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/1.quickcheck.badeof.bam /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/2.quickcheck.badheader.bam /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/3.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/4.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/6.quickcheck.cram21.ok.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/7.quickcheck.cram30.ok.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/8.quickcheck.cram21.truncated.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/9.quickcheck.cram30.truncated.cram /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok
test_quickcheck:
/builddir/build/BUILD/samtools-1.15.1/samtools quickcheck -uv /builddir/build/BUILD/samtools-1.15.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok
test_reheader:
/builddir/build/BUILD/samtools-1.15.1/samtools reheader /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/builddir/build/BUILD/samtools-1.15.1/samtools reheader /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v21.cram | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/builddir/build/BUILD/samtools-1.15.1/samtools reheader /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/builddir/build/BUILD/samtools-1.15.1/samtools reheader --in-place /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v21.cram && /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/builddir/build/BUILD/samtools-1.15.1/samtools reheader --in-place /builddir/build/BUILD/samtools-1.15.1/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v30.cram && /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/builddir/build/BUILD/samtools-1.15.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/builddir/build/BUILD/samtools-1.15.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.15.1/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//'
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -m orphan_only /builddir/build/BUILD/samtools-1.15.1/test/addrprg/2_fixup_orphan.sam
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -R '1#9' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -m orphan_only /builddir/build/BUILD/samtools-1.15.1/test/addrprg/2_fixup_orphan.sam
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -R '1#9' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/builddir/build/BUILD/samtools-1.15.1/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.15.1/test/addrprg/1_fixup.sam
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/1_name_sort.sam -
ERR: [markdup] error: queryname sorted, must be sorted by coordinate.
.. expected failure
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/2_bad_order.sam -
ERR: [markdup] error: not in coordinate sorted order.
.. expected failure
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/3_missing_mc.sam -
ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first.
[markdup] error: unable to assign pair hash key.
.. expected failure
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/4_missing_ms.sam -
ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first.
[markdup] error: no ms score tag. Please run samtools fixmate on file first.
.. expected failure
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/5_markdup.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -O sam -r --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/6_remove_dups.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/7_mark_supp_dup.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/8_optical_dup.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/9_optical_dup_qcfail.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/12_optical_chain_regex.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/1_name_sort.sam -
ERR: [markdup] error: queryname sorted, must be sorted by coordinate.
.. expected failure
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/2_bad_order.sam -
ERR: [markdup] error: not in coordinate sorted order.
.. expected failure
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/3_missing_mc.sam -
ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first.
[markdup] error: unable to assign pair hash key.
.. expected failure
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/4_missing_ms.sam -
ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first.
[markdup] error: no ms score tag. Please run samtools fixmate on file first.
.. expected failure
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/5_markdup.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -O sam -r --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/6_remove_dups.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/7_mark_supp_dup.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/8_optical_dup.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/9_optical_dup_qcfail.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /builddir/build/BUILD/samtools-1.15.1/test/markdup/10_optical_chain.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/11_optical_dup_regex.sam -
.. ok
test_markdup:
/builddir/build/BUILD/samtools-1.15.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /builddir/build/BUILD/samtools-1.15.1/test/markdup/12_optical_chain_regex.sam -
.. ok
test_bedcov:
/builddir/build/BUILD/samtools-1.15.1/samtools bedcov /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bam
.. ok
test_bedcov:
/builddir/build/BUILD/samtools-1.15.1/samtools bedcov -j /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bam
.. ok
test_bedcov:
/builddir/build/BUILD/samtools-1.15.1/samtools bedcov -g512 -G2048 /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.15.1/test/bedcov/bedcov.bam
.. ok
test_split:
/builddir/build/BUILD/samtools-1.15.1/samtools split --output-fmt sam -u /builddir/build/BUILD/samtools-1.15.1/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.15.1/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.15.1/test/split/split.sam
.. ok
test_split:
/builddir/build/BUILD/samtools-1.15.1/samtools split -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.15.1/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.15.1/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.15.1/test/split/split.sam
.. ok
test_large_positions:
/builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /tmp/r5Evz6CSKz/longref.sam.gz
.. ok
test_large_positions:
/builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /tmp/r5Evz6CSKz/longref.sam.gz CHROMOSOME_I:10000000114-10000000168
.. ok
test_large_positions:
/builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG -L /builddir/build/BUILD/samtools-1.15.1/test/large_pos/test.bed /tmp/r5Evz6CSKz/longref.sam.gz
.. ok
test_large_positions:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -O sam --no-PG -m 10M /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref_name.sam
.. ok
test_large_positions:
/builddir/build/BUILD/samtools-1.15.1/samtools merge -O sam --no-PG - /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref.sam /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref2.sam
.. ok
test_large_positions:
/builddir/build/BUILD/samtools-1.15.1/samtools depth /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref.sam
.. ok
test_large_positions:
/builddir/build/BUILD/samtools-1.15.1/samtools depth -b /builddir/build/BUILD/samtools-1.15.1/test/large_pos/test.bed /builddir/build/BUILD/samtools-1.15.1/test/large_pos/longref.sam
.. ok
test_large_positions:
/builddir/build/BUILD/samtools-1.15.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/r5Evz6CSKz/longref.sam.gz
.. ok
test_large_positions:
/builddir/build/BUILD/samtools-1.15.1/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam |
/builddir/build/BUILD/samtools-1.15.1/samtools fixmate -O sam --no-PG - - |
/builddir/build/BUILD/samtools-1.15.1/samtools sort -O sam --no-PG -m 10M
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/2_both_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_test_data.sam
.. ok
test_ampliconclip:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/2_both_test_data.sam
.. ok
test_ampliconstats:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_hard_clipped.expected.sam /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_soft_clipped.expected.sam /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/1_soft_clipped_strand.expected.sam /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/2_both_clipped.expected.sam | egrep -v 'Samtools version|Command line'
.. ok
test_ampliconstats:
/builddir/build/BUILD/samtools-1.15.1/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.15.1/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.15.1/test/ampliconstats/mixed_clipped.sam | egrep -v 'Samtools version|Command line'
.. ok
Number of tests:
total .. 807
passed .. 776
failed .. 0
expected failure .. 31
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
cd test/mpileup && AWK="gawk" ../regression.sh mpileup.reg
=== Testing mpileup.reg regressions ===
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam
Expected passes: 118
Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
cd test/mpileup && AWK="gawk" ../regression.sh depth.reg
=== Testing depth.reg regressions ===
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools depth -a -b xx.bed3 xx#depth3.bam
Expected passes: 47
Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
cd test/consensus && AWK="gawk" ../regression.sh consensus.reg
=== Testing consensus.reg regressions ===
Expected passes: 62
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
=> PASS
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: samtools-1.15.1-1.fc38.ppc64le
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.4ONmYu
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ DOCDIR=/builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/share/doc/samtools
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/share/doc/samtools
+ cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/share/doc/samtools
+ cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/share/doc/samtools
+ cp -pr NEWS /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/share/doc/samtools
+ cp -pr examples/ /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/share/doc/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.JxEm3A
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/share/licenses/samtools
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/share/licenses/samtools
+ cp -pr LICENSE /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le/usr/share/licenses/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: samtools = 1.15.1-1.fc38 samtools(ppc-64) = 1.15.1-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl ld64.so.2()(64bit) ld64.so.2(GLIBC_2.23)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Processing files: samtools-debugsource-1.15.1-1.fc38.ppc64le
Provides: samtools-debugsource = 1.15.1-1.fc38 samtools-debugsource(ppc-64) = 1.15.1-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: samtools-debuginfo-1.15.1-1.fc38.ppc64le
Provides: debuginfo(build-id) = 17c7145200cd0f6b1e10f79bf9640533be9100ee debuginfo(build-id) = 1cbae4bf9cb9a273c243ad813baa65514d7c49b9 debuginfo(build-id) = 81a987f09864f201f2086f65506c1e8f2249baf3 debuginfo(build-id) = 865cad001f9b789b7a66cf2102be4ed759bcc325 debuginfo(build-id) = 88d4cc3647f0085612e3713650edbd26f8d18f26 debuginfo(build-id) = adae7fb87da379dcbbede34dc5c54e31f69370ae debuginfo(build-id) = bd1c20b024d17c0cc727d9c771004ae1cce5ed5e samtools-debuginfo = 1.15.1-1.fc38 samtools-debuginfo(ppc-64) = 1.15.1-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: samtools-debugsource(ppc-64) = 1.15.1-1.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le
Wrote: /builddir/build/RPMS/samtools-1.15.1-1.fc38.ppc64le.rpm
Wrote: /builddir/build/RPMS/samtools-debugsource-1.15.1-1.fc38.ppc64le.rpm
Wrote: /builddir/build/RPMS/samtools-debuginfo-1.15.1-1.fc38.ppc64le.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.h6keM0
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.ppc64le
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.LEXmtM
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf samtools-1.15.1 samtools-1.15.1.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0