Mock Version: 3.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target x86_64 --nodeps /builddir/build/SPECS/samtools.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1672304844.988018/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 0x7fac2e31ea50>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.cr_f6edx:/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.cr_f6edx:/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', '503c4f2f81a14ecb8e774f1e0d363afa', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1672304844.988018/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.cr_f6edx:/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 x86_64 --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: x86_64
Building for target x86_64
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 x86_64 --nodeps /builddir/build/SPECS/samtools.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1672304844.988018/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 0x7fac2e31ea50>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.cr_f6edx:/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.cr_f6edx:/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', '04af193ea2d946f392c99bfa341d0980', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1672304844.988018/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.cr_f6edx:/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 x86_64 --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: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1660521600
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.Gw7QlA
+ 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.S4Sosi
+ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 09:09:11.814408389 +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=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 x86_64-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 -j2 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o test/split/test_parse_args.o test/split/test_parse_args.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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I.  -I./lz4  -c -o bamtk.o bamtk.c
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o
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 -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 -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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 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/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 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/merge/test_rtrans_build test/merge/test_rtrans_build.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_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 test/split/test_filter_header_rg test/split/test_filter_header_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/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 test/vcf-miniview test/vcf-miniview.o -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_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 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.2W9eiT
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64
++ dirname /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64
+ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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.x86_64 'INSTALL=/usr/bin/install -p'
mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/man/man1
/usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/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.x86_64/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.x86_64/usr/bin
/usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/man/man1
++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/zoom2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/blast2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/bowtie2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/export2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/fasta-sanitize.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/interpolate_sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/novo2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/plot-ampliconstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/plot-bamstats
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/psl2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/sam2vcf.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/samtools.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/seq_cache_populate.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/soap2sam.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/wgsim_eval.pl
+ for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/*)
+ sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/zoom2sam.pl
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.15.1-1.fc38 --unique-debug-suffix -1.15.1-1.fc38.x86_64 --unique-debug-src-base samtools-1.15.1-1.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.15.1
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/maq2sam-long
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/ace2sam
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/maq2sam-short
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/md5fa
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/md5sum-lite
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/samtools
extracting debug info from /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/bin/wgsim
original debug info size: 2072kB, size after compression: 1876kB
/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.Ttz5mv
+ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 (0x00007f530c134000)
+ 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/KzfAmRrDd1/bgzip.dat.gz
.. ok
bgzip -c -b 979200 -s 6 /tmp/KzfAmRrDd1/bgzip.dat.gz
.. ok
bgzip -c -b 652804 -s 6 /tmp/KzfAmRrDd1/bgzip.dat.gz
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/KzfAmRrDd1/faidx.fa 3:11-13 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/KzfAmRrDd1/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/KzfAmRrDd1/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/KzfAmRrDd1/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/KzfAmRrDd1/faidx.fa 1:100-104 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/KzfAmRrDd1/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/KzfAmRrDd1/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools faidx /tmp/KzfAmRrDd1/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/KzfAmRrDd1/fqidx.fq 3:11-13
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/KzfAmRrDd1/fqidx.fq.gz 3:11-13
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/KzfAmRrDd1/fqidx.fq 2:998-1003
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/KzfAmRrDd1/fqidx.fq.gz 2:998-1003
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/KzfAmRrDd1/fqidx.fq 1:100-104
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/KzfAmRrDd1/fqidx.fq.gz 1:100-104
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/KzfAmRrDd1/fqidx.fq 1:99998-100007
.. ok
.. ok
/builddir/build/BUILD/samtools-1.15.1/samtools fqidx /tmp/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/large_chrom.bam ref2
.. ok
test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools view /tmp/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/auto_indexed.csi && cat /tmp/KzfAmRrDd1/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/KzfAmRrDd1/auto_indexed.crai && cat /tmp/KzfAmRrDd1/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/KzfAmRrDd1/auto_indexed.csi && cat /tmp/KzfAmRrDd1/auto_indexed.csi
.. ok
test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/KzfAmRrDd1/large_chrom.bam ref2
.. ok
test_index:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -@ 2 /tmp/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/auto_indexed.csi && cat /tmp/KzfAmRrDd1/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/KzfAmRrDd1/auto_indexed.crai && cat /tmp/KzfAmRrDd1/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/KzfAmRrDd1/auto_indexed.csi && cat /tmp/KzfAmRrDd1/auto_indexed.csi
.. ok
test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/KzfAmRrDd1/mpileup.bam.list -f /tmp/KzfAmRrDd1/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/KzfAmRrDd1/mpileup.cram.list -f /tmp/KzfAmRrDd1/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/KzfAmRrDd1/mpileup.bam.urllist -f /tmp/KzfAmRrDd1/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -b /tmp/KzfAmRrDd1/mpileup.cram.urllist -f /tmp/KzfAmRrDd1/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/KzfAmRrDd1/mpileup.ref.fa.gz -r17:1050-1060 /tmp/KzfAmRrDd1/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
	/builddir/build/BUILD/samtools-1.15.1/samtools mpileup -B --ff 0x14 -f /tmp/KzfAmRrDd1/mpileup.ref.fa.gz -r17:1050-1060 /tmp/KzfAmRrDd1/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/KzfAmRrDd1/view.001.fogn (SAM input)     .. ok
	50: Count -R /tmp/KzfAmRrDd1/view.001.fogn (SAM input)      .. ok
	51: Filter -R /tmp/KzfAmRrDd1/view.001.fogn (BAM input)     .. ok
	52: Count -R /tmp/KzfAmRrDd1/view.001.fogn (BAM input)      .. ok
	53: Filter -R /tmp/KzfAmRrDd1/view.001.fogn (CRAM input)    .. ok
	54: Count -R /tmp/KzfAmRrDd1/view.001.fogn (CRAM input)     .. ok
	55: Filter -R /tmp/KzfAmRrDd1/view.001.fogn -r grp2 (SAM input).. ok
	56: Count -R /tmp/KzfAmRrDd1/view.001.fogn -r grp2 (SAM input).. ok
	57: Filter -R /tmp/KzfAmRrDd1/view.001.fogn -r grp2 (BAM input).. ok
	58: Count -R /tmp/KzfAmRrDd1/view.001.fogn -r grp2 (BAM input).. ok
	59: Filter -R /tmp/KzfAmRrDd1/view.001.fogn -r grp2 (CRAM input).. ok
	60: Count -R /tmp/KzfAmRrDd1/view.001.fogn -r grp2 (CRAM input).. ok
	61: Filter -r grp2 -R /tmp/KzfAmRrDd1/view.001.fogn (SAM input).. ok
	62: Count -r grp2 -R /tmp/KzfAmRrDd1/view.001.fogn (SAM input).. ok
	63: Filter -r grp2 -R /tmp/KzfAmRrDd1/view.001.fogn (BAM input).. ok
	64: Count -r grp2 -R /tmp/KzfAmRrDd1/view.001.fogn (BAM input).. ok
	65: Filter -r grp2 -R /tmp/KzfAmRrDd1/view.001.fogn (CRAM input).. ok
	66: Count -r grp2 -R /tmp/KzfAmRrDd1/view.001.fogn (CRAM input).. ok
	67: Filter -N /tmp/KzfAmRrDd1/view.001.forn (SAM input)     .. ok
	68: Count -N /tmp/KzfAmRrDd1/view.001.forn (SAM input)      .. ok
	69: Filter -N /tmp/KzfAmRrDd1/view.001.forn (BAM input)     .. ok
	70: Count -N /tmp/KzfAmRrDd1/view.001.forn (BAM input)      .. ok
	71: Filter -N /tmp/KzfAmRrDd1/view.001.forn (CRAM input)    .. ok
	72: Count -N /tmp/KzfAmRrDd1/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/KzfAmRrDd1/view.001.fobc (SAM input)  .. ok
	86: Count -D BC:/tmp/KzfAmRrDd1/view.001.fobc (SAM input)   .. ok
	87: Filter -D BC:/tmp/KzfAmRrDd1/view.001.fobc (BAM input)  .. ok
	88: Count -D BC:/tmp/KzfAmRrDd1/view.001.fobc (BAM input)   .. ok
	89: Filter -D BC:/tmp/KzfAmRrDd1/view.001.fobc (CRAM input) .. ok
	90: Count -D BC:/tmp/KzfAmRrDd1/view.001.fobc (CRAM input)  .. ok
	91: Filter -D BC:/tmp/KzfAmRrDd1/view.001.fobc -d BC:TGCA (SAM input).. ok
	92: Count -D BC:/tmp/KzfAmRrDd1/view.001.fobc -d BC:TGCA (SAM input).. ok
	93: Filter -D BC:/tmp/KzfAmRrDd1/view.001.fobc -d BC:TGCA (BAM input).. ok
	94: Count -D BC:/tmp/KzfAmRrDd1/view.001.fobc -d BC:TGCA (BAM input).. ok
	95: Filter -D BC:/tmp/KzfAmRrDd1/view.001.fobc -d BC:TGCA (CRAM input).. ok
	96: Count -D BC:/tmp/KzfAmRrDd1/view.001.fobc -d BC:TGCA (CRAM input).. ok
	97: Filter -d BC:TGCA -D BC:/tmp/KzfAmRrDd1/view.001.fobc (SAM input).. ok
	98: Count -d BC:TGCA -D BC:/tmp/KzfAmRrDd1/view.001.fobc (SAM input).. ok
	99: Filter -d BC:TGCA -D BC:/tmp/KzfAmRrDd1/view.001.fobc (BAM input).. ok
	100: Count -d BC:TGCA -D BC:/tmp/KzfAmRrDd1/view.001.fobc (BAM input).. ok
	101: Filter -d BC:TGCA -D BC:/tmp/KzfAmRrDd1/view.001.fobc (CRAM input).. ok
	102: Count -d BC:TGCA -D BC:/tmp/KzfAmRrDd1/view.001.fobc (CRAM input).. ok
	103: Filter -D RG:/tmp/KzfAmRrDd1/view.001.fogn (SAM input) .. ok
	104: Count -D RG:/tmp/KzfAmRrDd1/view.001.fogn (SAM input)  .. ok
	105: Filter -D RG:/tmp/KzfAmRrDd1/view.001.fogn (BAM input) .. ok
	106: Count -D RG:/tmp/KzfAmRrDd1/view.001.fogn (BAM input)  .. ok
	107: Filter -D RG:/tmp/KzfAmRrDd1/view.001.fogn (CRAM input).. ok
	108: Count -D RG:/tmp/KzfAmRrDd1/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/KzfAmRrDd1/view.test115.sam -h -d TGCA /tmp/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/view.test117.sam -h -d TGCA /tmp/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/view.test119.sam -h -d TGCA /tmp/KzfAmRrDd1/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/KzfAmRrDd1/view.test006.cram --no-PG
.. expected failure
	121: Filter -D BClong:/tmp/KzfAmRrDd1/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/KzfAmRrDd1/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/KzfAmRrDd1/view.test121.sam -h -D BClong:/tmp/KzfAmRrDd1/view.001.fobc /tmp/KzfAmRrDd1/view.001.sam --no-PG
.. expected failure
	122: Count -D BClong:/tmp/KzfAmRrDd1/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/KzfAmRrDd1/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/KzfAmRrDd1/view.001.fobc /tmp/KzfAmRrDd1/view.001.sam --no-PG
.. expected failure
	123: Filter -D BClong:/tmp/KzfAmRrDd1/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/KzfAmRrDd1/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/KzfAmRrDd1/view.test123.sam -h -D BClong:/tmp/KzfAmRrDd1/view.001.fobc /tmp/KzfAmRrDd1/view.test001.bam --no-PG
.. expected failure
	124: Count -D BClong:/tmp/KzfAmRrDd1/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/KzfAmRrDd1/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/KzfAmRrDd1/view.001.fobc /tmp/KzfAmRrDd1/view.test001.bam --no-PG
.. expected failure
	125: Filter -D BClong:/tmp/KzfAmRrDd1/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/KzfAmRrDd1/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -o /tmp/KzfAmRrDd1/view.test125.sam -h -D BClong:/tmp/KzfAmRrDd1/view.001.fobc /tmp/KzfAmRrDd1/view.test006.cram --no-PG
.. expected failure
	126: Count -D BClong:/tmp/KzfAmRrDd1/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/KzfAmRrDd1/view.001.fobc"
	Failed command:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -c -D BClong:/tmp/KzfAmRrDd1/view.001.fobc /tmp/KzfAmRrDd1/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/KzfAmRrDd1/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/bam2fq.discard.s.fq -0 /tmp/KzfAmRrDd1/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/KzfAmRrDd1/bam2fq.discard.s.fq -0 /tmp/KzfAmRrDd1/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/rAMfOHQcaZ - /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/KzfAmRrDd1/merge.tag.1.bam /tmp/KzfAmRrDd1/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/KzfAmRrDd1/merge.tag.3.bam /tmp/KzfAmRrDd1/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/KzfAmRrDd1/merge.bed.1.bam /tmp/KzfAmRrDd1/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/6EkP9QIXTR - /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/KzfAmRrDd1/merge.tag.1.bam /tmp/KzfAmRrDd1/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/KzfAmRrDd1/merge.tag.3.bam /tmp/KzfAmRrDd1/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/KzfAmRrDd1/merge.bed.1.bam /tmp/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/longref.sam.gz
.. ok
test_large_positions:
	/builddir/build/BUILD/samtools-1.15.1/samtools view -h --no-PG /tmp/KzfAmRrDd1/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/KzfAmRrDd1/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/KzfAmRrDd1/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.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.QSHy5h
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ DOCDIR=/builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/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.x86_64/usr/share/doc/samtools
+ cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/doc/samtools
+ cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/doc/samtools
+ cp -pr NEWS /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/doc/samtools
+ cp -pr examples/ /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/doc/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.5EK6WL
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/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.x86_64/usr/share/licenses/samtools
+ cp -pr LICENSE /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64/usr/share/licenses/samtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: samtools = 1.15.1-1.fc38 samtools(x86-64) = 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 libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(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.x86_64
Provides: samtools-debugsource = 1.15.1-1.fc38 samtools-debugsource(x86-64) = 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.x86_64
Provides: debuginfo(build-id) = 2e56ae12cfd411515abd2c4304253d785aedce72 debuginfo(build-id) = 3aaca2212e2f7e47ef76b60b999889a6195e2d62 debuginfo(build-id) = 6f8469bf986d2d3750230bc5d2eb44cc15e333d4 debuginfo(build-id) = b1f490018a69f8dc102e48e2105850282dc6c255 debuginfo(build-id) = b40b7e6be806c9881986b339934282ba7c30ac24 debuginfo(build-id) = b4da38ed499cc125a2adaabc8ed5c69e2013bbb4 debuginfo(build-id) = e70ed15a7431e385acf0193076b74c06c76a6def samtools-debuginfo = 1.15.1-1.fc38 samtools-debuginfo(x86-64) = 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(x86-64) = 1.15.1-1.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64
Wrote: /builddir/build/RPMS/samtools-1.15.1-1.fc38.x86_64.rpm
Wrote: /builddir/build/RPMS/samtools-debuginfo-1.15.1-1.fc38.x86_64.rpm
Wrote: /builddir/build/RPMS/samtools-debugsource-1.15.1-1.fc38.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.vVh6DM
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-1.15.1
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.15.1-1.fc38.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.mSX5Oe
+ 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