Mock Version: 5.6 Mock Version: 5.6 Mock Version: 5.6 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target aarch64 --nodeps /builddir/build/SPECS/htslib.spec'], chrootPath='/var/lib/mock/f42-build-54727542-6528772/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.1p3mz7tj:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.1p3mz7tj:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', '1e16f7d3c81647a4844bad02b5e0a4ff', '-D', '/var/lib/mock/f42-build-54727542-6528772/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.1p3mz7tj:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target aarch64 --nodeps /builddir/build/SPECS/htslib.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721260800 Wrote: /builddir/build/SRPMS/htslib-1.15.1-6.fc42.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target aarch64 --nodeps /builddir/build/SPECS/htslib.spec'], chrootPath='/var/lib/mock/f42-build-54727542-6528772/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.1p3mz7tj:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.1p3mz7tj:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', 'cdea448e8f3842ef84c3ef4368b42cfb', '-D', '/var/lib/mock/f42-build-54727542-6528772/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.1p3mz7tj:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target aarch64 --nodeps /builddir/build/SPECS/htslib.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721260800 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.fiBuqn + umask 022 + cd /builddir/build/BUILD/htslib-1.15.1-build + test -d /builddir/build/BUILD/htslib-1.15.1-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/htslib-1.15.1-build + /usr/bin/rm -rf /builddir/build/BUILD/htslib-1.15.1-build + /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.15.1-build + /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.15.1-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.H4psPb + umask 022 + cd /builddir/build/BUILD/htslib-1.15.1-build + cd /builddir/build/BUILD/htslib-1.15.1-build + rm -rf htslib-1.15.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/htslib-1.15.1.tar.bz2 + STATUS=0 + '[' 0 -ne 0 ']' + cd htslib-1.15.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (htslib-1.15.1-gcc12.patch): + echo 'Patch #0 (htslib-1.15.1-gcc12.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file htscodecs/htscodecs/rANS_word.h + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.USp0i1 + umask 022 + cd /builddir/build/BUILD/htslib-1.15.1-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 htslib-1.15.1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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' ./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 --- ./configure.backup 2022-04-07 15:42:52.000000000 +0000 +++ ./configure 2024-11-04 17:41:31.434752161 +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' ./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* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=aarch64-redhat-linux-gnu --host=aarch64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' --prefix=/usr --libdir=/usr/lib64 --enable-plugins '--with-plugin-path=/usr/local/libexec/htslib:$(plugindir)' --enable-gcs --enable-libcurl --enable-s3 configure: WARNING: unrecognized options: --disable-dependency-tracking checking for aarch64-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 aarch64-redhat-linux-gnu-ranlib... no checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for aarch64-redhat-linux-gnu-pkg-config... /usr/bin/aarch64-redhat-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for aarch64-redhat-linux-gnu... plain .so checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing dlsym... none required checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for library containing regcomp... none required checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk configure: WARNING: unrecognized options: --disable-dependency-tracking + /usr/bin/make -O -j12 V=1 VERBOSE=1 echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h echo '#define HTS_CC "gcc"' > config_vars.h echo '#define HTS_CPPFLAGS ""' >> config_vars.h echo '#define HTS_CFLAGS "-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden"' >> config_vars.h echo '#define HTS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic"' >> config_vars.h echo '#define HTS_LIBS "-llzma -lbz2 -lz -lm "' >> config_vars.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o hts_os.o hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o kfunc.o kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o multipart.o multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o md5.o md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o errmod.o errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o kstring.o kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o probaln.o probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o region.o region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o realn.o realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o hfile.o hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o faidx.o faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o tbx.o tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o textutils.o textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o bgzf.o bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o header.o header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -c -o plugin.o plugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o region.pico region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o header.pico header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o sam.o sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o vcf.o vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -DPLUGINPATH=\"/usr/local/libexec/htslib:/usr/libexec/htslib\" -fpic -c -o plugin.pico plugin.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o bgzip.o bgzip.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o htsfile.o htsfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o tabix.o tabix.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile_s3_write.pico hfile_s3_write.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c hfile_libcurl.c: In function ‘libcurl_open’: hfile_libcurl.c:1335:9: warning: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’ is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD, | ^~ In file included from hfile_libcurl.c:47: /usr/include/curl/curl.h:2892:3: note: declared here 2892 | CURLINFO_CONTENT_LENGTH_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o test/sam.o test/sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -c -o hts.o hts.c ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o plugin.o ranlib libhts.a gcc -shared -Wl,-soname,libhts.so.3 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico plugin.pico -llzma -lbz2 -lz -lm -lpthread ln -sf libhts.so libhts.so.3 gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -llzma -lbz2 -lz -lm -lcrypto -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread + sed -i -E '/^(Libs|Requires)\.private:/d' htslib.pc.tmp + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.zT3RFV + umask 022 + cd /builddir/build/BUILD/htslib-1.15.1-build + '[' /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT ++ dirname /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT + mkdir -p /builddir/build/BUILD/htslib-1.15.1-build + mkdir /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 htslib-1.15.1 + /usr/bin/make install DESTDIR=/builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/bin /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/include /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/include/htslib /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/man/man1 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/man/man5 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/man/man7 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/pkgconfig if test -n "/usr/libexec/htslib"; then mkdir -p -m 755 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/libexec/htslib; fi /usr/bin/install -p -m 644 libhts.so /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/libhts.so.1.15.1 ln -sf libhts.so.1.15.1 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/libhts.so ln -sf libhts.so.1.15.1 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/libhts.so.3 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib64#g;s#@-PACKAGE_VERSION@#1.15.1#g' htslib.pc.tmp > /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/pkgconfig/htslib.pc chmod 644 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/pkgconfig/htslib.pc /usr/bin/install -p bgzip htsfile tabix /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then /usr/bin/install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/libexec/htslib; fi /usr/bin/install -p -m 644 htslib/*.h /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/include/htslib /usr/bin/install -p -m 644 libhts.a /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64/libhts.a /usr/bin/install -p -m 644 bgzip.1 htsfile.1 tabix.1 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/man/man1 /usr/bin/install -p -m 644 faidx.5 sam.5 vcf.5 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/man/man5 /usr/bin/install -p -m 644 htslib-s3-plugin.7 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/man/man7 + pushd /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT//usr/lib64 + chmod 755 libhts.so.1.15.1 ~/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/lib64 ~/build/BUILD/htslib-1.15.1-build/htslib-1.15.1 + popd ~/build/BUILD/htslib-1.15.1-build/htslib-1.15.1 + find /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT -name '*.la' -delete + rm -f /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT//usr/lib64/libhts.a + /usr/bin/find-debuginfo -j12 --strict-build-id -m -i --build-id-seed 1.15.1-6.fc42 --unique-debug-suffix -1.15.1-6.fc42.aarch64 --unique-debug-src-base htslib-1.15.1-6.fc42.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1 find-debuginfo: starting Extracting debug info from 8 files DWARF-compressing 8 files sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/htslib-1.15.1-6.fc42.aarch64 find-debuginfo: done + /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 + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j12 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j12 /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT Scanned 29 directories and 162 files, processed 0 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/htslib-1.15.1-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.TKMCFp + umask 022 + cd /builddir/build/BUILD/htslib-1.15.1-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 htslib-1.15.1 + make test gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/rANS_static_test.o htscodecs/tests/rANS_static_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x8 htscodecs/tests/rANS_static_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x8.test Testing rans4x8 -r -o0 on ./dat/q4 11674 Testing rans4x8 -r -o1 on ./dat/q4 10870 Testing rans4x8 -r -o0 on ./dat/q40+dir 50258 Testing rans4x8 -r -o1 on ./dat/q40+dir 50537 Testing rans4x8 -r -o0 on ./dat/q8 33099 Testing rans4x8 -r -o1 on ./dat/q8 31428 Testing rans4x8 -r -o0 on ./dat/qvar 32997 Testing rans4x8 -r -o1 on ./dat/qvar 32832 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/rANS_static4x16pr_test.o htscodecs/tests/rANS_static4x16pr_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o htscodecs/tests/rans4x16pr htscodecs/tests/rANS_static4x16pr_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x16.test Testing rans4x16 -r -o0 on ./dat/q4 11660 Testing rans4x16 -r -o1 on ./dat/q4 10848 Testing rans4x16 -r -o64 on ./dat/q4 12878 Testing rans4x16 -r -o65 on ./dat/q4 10672 Testing rans4x16 -r -o128 on ./dat/q4 10902 Testing rans4x16 -r -o129 on ./dat/q4 10890 Testing rans4x16 -r -o192 on ./dat/q4 11225 Testing rans4x16 -r -o193 on ./dat/q4 10825 Testing rans4x16 -r -o8 on ./dat/q4 11731 Testing rans4x16 -r -o9 on ./dat/q4 11111 Testing rans4x16 -r -o0 on ./dat/q40+dir 50247 Testing rans4x16 -r -o1 on ./dat/q40+dir 49449 Testing rans4x16 -r -o8 on ./dat/q40+dir 50072 Testing rans4x16 -r -o9 on ./dat/q40+dir 50072 Testing rans4x16 -r -o0 on ./dat/q8 33088 Testing rans4x16 -r -o1 on ./dat/q8 31372 Testing rans4x16 -r -o64 on ./dat/q8 33458 Testing rans4x16 -r -o65 on ./dat/q8 31025 Testing rans4x16 -r -o128 on ./dat/q8 32237 Testing rans4x16 -r -o129 on ./dat/q8 31258 Testing rans4x16 -r -o192 on ./dat/q8 32024 Testing rans4x16 -r -o193 on ./dat/q8 31146 Testing rans4x16 -r -o0 on ./dat/qvar 32987 Testing rans4x16 -r -o1 on ./dat/qvar 32261 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/arith_dynamic_test.o htscodecs/tests/arith_dynamic_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o htscodecs/tests/arith_dynamic htscodecs/tests/arith_dynamic_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./arith.test Testing arith_dynamic -r -o0 on ./dat/q4 11615 Testing arith_dynamic -r -o1 on ./dat/q4 10831 Testing arith_dynamic -r -o64 on ./dat/q4 13360 Testing arith_dynamic -r -o65 on ./dat/q4 10484 Testing arith_dynamic -r -o128 on ./dat/q4 10774 Testing arith_dynamic -r -o129 on ./dat/q4 10329 Testing arith_dynamic -r -o192 on ./dat/q4 11095 Testing arith_dynamic -r -o193 on ./dat/q4 10283 Testing arith_dynamic -r -o8 on ./dat/q4 11448 Testing arith_dynamic -r -o9 on ./dat/q4 11083 Testing arith_dynamic -r -o0 on ./dat/q40+dir 49949 Testing arith_dynamic -r -o1 on ./dat/q40+dir 49034 Testing arith_dynamic -r -o64 on ./dat/q40+dir 51242 Testing arith_dynamic -r -o65 on ./dat/q40+dir 49061 Testing arith_dynamic -r -o8 on ./dat/q40+dir 49820 Testing arith_dynamic -r -o9 on ./dat/q40+dir 49448 Testing arith_dynamic -r -o0 on ./dat/q8 32752 Testing arith_dynamic -r -o1 on ./dat/q8 31331 Testing arith_dynamic -r -o64 on ./dat/q8 35211 Testing arith_dynamic -r -o65 on ./dat/q8 30907 Testing arith_dynamic -r -o128 on ./dat/q8 32063 Testing arith_dynamic -r -o129 on ./dat/q8 31084 Testing arith_dynamic -r -o192 on ./dat/q8 32267 Testing arith_dynamic -r -o193 on ./dat/q8 30931 Testing arith_dynamic -r -o0 on ./dat/qvar 32597 Testing arith_dynamic -r -o1 on ./dat/qvar 31982 Testing arith_dynamic -r -o64 on ./dat/qvar 33237 Testing arith_dynamic -r -o65 on ./dat/qvar 31993 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/tokenise_name3_test.o htscodecs/tests/tokenise_name3_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o htscodecs/tests/tokenise_name3 htscodecs/tests/tokenise_name3_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./tok3.test Testing tokenise_name3 -r -1 on ./names/01.names 3392 Testing tokenise_name3 -r -3 on ./names/01.names 2471 Testing tokenise_name3 -r -5 on ./names/01.names 2283 Testing tokenise_name3 -r -7 on ./names/01.names 2234 Testing tokenise_name3 -r -9 on ./names/01.names 2234 Testing tokenise_name3 -r -11 on ./names/01.names 3151 Testing tokenise_name3 -r -13 on ./names/01.names 2424 Testing tokenise_name3 -r -15 on ./names/01.names 2061 Testing tokenise_name3 -r -17 on ./names/01.names 2051 Testing tokenise_name3 -r -19 on ./names/01.names 2049 Testing tokenise_name3 -r -1 on ./names/02.names 6633 Testing tokenise_name3 -r -3 on ./names/02.names 4983 Testing tokenise_name3 -r -5 on ./names/02.names 4942 Testing tokenise_name3 -r -7 on ./names/02.names 4922 Testing tokenise_name3 -r -9 on ./names/02.names 4918 Testing tokenise_name3 -r -11 on ./names/02.names 6087 Testing tokenise_name3 -r -13 on ./names/02.names 4797 Testing tokenise_name3 -r -15 on ./names/02.names 4714 Testing tokenise_name3 -r -17 on ./names/02.names 4695 Testing tokenise_name3 -r -19 on ./names/02.names 4695 Testing tokenise_name3 -r -1 on ./names/03.names 10557 Testing tokenise_name3 -r -3 on ./names/03.names 7822 Testing tokenise_name3 -r -5 on ./names/03.names 7557 Testing tokenise_name3 -r -7 on ./names/03.names 7521 Testing tokenise_name3 -r -9 on ./names/03.names 7521 Testing tokenise_name3 -r -11 on ./names/03.names 9294 Testing tokenise_name3 -r -13 on ./names/03.names 7291 Testing tokenise_name3 -r -15 on ./names/03.names 7125 Testing tokenise_name3 -r -17 on ./names/03.names 7069 Testing tokenise_name3 -r -19 on ./names/03.names 7068 Testing tokenise_name3 -r -1 on ./names/05.names 5098 Testing tokenise_name3 -r -3 on ./names/05.names 3600 Testing tokenise_name3 -r -5 on ./names/05.names 3551 Testing tokenise_name3 -r -7 on ./names/05.names 3534 Testing tokenise_name3 -r -9 on ./names/05.names 3534 Testing tokenise_name3 -r -11 on ./names/05.names 4648 Testing tokenise_name3 -r -13 on ./names/05.names 3405 Testing tokenise_name3 -r -15 on ./names/05.names 3381 Testing tokenise_name3 -r -17 on ./names/05.names 3377 Testing tokenise_name3 -r -19 on ./names/05.names 3377 Testing tokenise_name3 -r -1 on ./names/08.names 6841 Testing tokenise_name3 -r -3 on ./names/08.names 5291 Testing tokenise_name3 -r -5 on ./names/08.names 5206 Testing tokenise_name3 -r -7 on ./names/08.names 5160 Testing tokenise_name3 -r -9 on ./names/08.names 5160 Testing tokenise_name3 -r -11 on ./names/08.names 6374 Testing tokenise_name3 -r -13 on ./names/08.names 4895 Testing tokenise_name3 -r -15 on ./names/08.names 4851 Testing tokenise_name3 -r -17 on ./names/08.names 4805 Testing tokenise_name3 -r -19 on ./names/08.names 4805 Testing tokenise_name3 -r -1 on ./names/09.names 5339 Testing tokenise_name3 -r -3 on ./names/09.names 3598 Testing tokenise_name3 -r -5 on ./names/09.names 3527 Testing tokenise_name3 -r -7 on ./names/09.names 3493 Testing tokenise_name3 -r -9 on ./names/09.names 3493 Testing tokenise_name3 -r -11 on ./names/09.names 4861 Testing tokenise_name3 -r -13 on ./names/09.names 3427 Testing tokenise_name3 -r -15 on ./names/09.names 3391 Testing tokenise_name3 -r -17 on ./names/09.names 3366 Testing tokenise_name3 -r -19 on ./names/09.names 3366 Testing tokenise_name3 -r -1 on ./names/10.names 6458 Testing tokenise_name3 -r -3 on ./names/10.names 4843 Testing tokenise_name3 -r -5 on ./names/10.names 4799 Testing tokenise_name3 -r -7 on ./names/10.names 4746 Testing tokenise_name3 -r -9 on ./names/10.names 4744 Testing tokenise_name3 -r -11 on ./names/10.names 5785 Testing tokenise_name3 -r -13 on ./names/10.names 4567 Testing tokenise_name3 -r -15 on ./names/10.names 4492 Testing tokenise_name3 -r -17 on ./names/10.names 4472 Testing tokenise_name3 -r -19 on ./names/10.names 4472 Testing tokenise_name3 -r -1 on ./names/20.names 2511 Testing tokenise_name3 -r -3 on ./names/20.names 1701 Testing tokenise_name3 -r -5 on ./names/20.names 1659 Testing tokenise_name3 -r -7 on ./names/20.names 1632 Testing tokenise_name3 -r -9 on ./names/20.names 1632 Testing tokenise_name3 -r -11 on ./names/20.names 2319 Testing tokenise_name3 -r -13 on ./names/20.names 1629 Testing tokenise_name3 -r -15 on ./names/20.names 1605 Testing tokenise_name3 -r -17 on ./names/20.names 1600 Testing tokenise_name3 -r -19 on ./names/20.names 1600 Testing tokenise_name3 -r -1 on ./names/nv.names 6816 Testing tokenise_name3 -r -3 on ./names/nv.names 4989 Testing tokenise_name3 -r -5 on ./names/nv.names 4972 Testing tokenise_name3 -r -7 on ./names/nv.names 4937 Testing tokenise_name3 -r -9 on ./names/nv.names 4937 Testing tokenise_name3 -r -11 on ./names/nv.names 6084 Testing tokenise_name3 -r -13 on ./names/nv.names 4825 Testing tokenise_name3 -r -15 on ./names/nv.names 4771 Testing tokenise_name3 -r -17 on ./names/nv.names 4767 Testing tokenise_name3 -r -19 on ./names/nv.names 4767 Testing tokenise_name3 -r -1 on ./names/nv2.names 1181 Testing tokenise_name3 -r -3 on ./names/nv2.names 903 Testing tokenise_name3 -r -5 on ./names/nv2.names 879 Testing tokenise_name3 -r -7 on ./names/nv2.names 846 Testing tokenise_name3 -r -9 on ./names/nv2.names 846 Testing tokenise_name3 -r -11 on ./names/nv2.names 891 Testing tokenise_name3 -r -13 on ./names/nv2.names 836 Testing tokenise_name3 -r -15 on ./names/nv2.names 764 Testing tokenise_name3 -r -17 on ./names/nv2.names 747 Testing tokenise_name3 -r -19 on ./names/nv2.names 747 Testing tokenise_name3 -r -1 on ./names/rr.names 8788 Testing tokenise_name3 -r -3 on ./names/rr.names 6290 Testing tokenise_name3 -r -5 on ./names/rr.names 6252 Testing tokenise_name3 -r -7 on ./names/rr.names 6230 Testing tokenise_name3 -r -9 on ./names/rr.names 6230 Testing tokenise_name3 -r -11 on ./names/rr.names 8319 Testing tokenise_name3 -r -13 on ./names/rr.names 6066 Testing tokenise_name3 -r -15 on ./names/rr.names 5972 Testing tokenise_name3 -r -17 on ./names/rr.names 5963 Testing tokenise_name3 -r -19 on ./names/rr.names 5963 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/fqzcomp_qual_test.o htscodecs/tests/fqzcomp_qual_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o htscodecs/tests/fqzcomp_qual htscodecs/tests/fqzcomp_qual_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && srcdir=. && export srcdir && ./fqzcomp.test Testing fqzcomp_qual -r -s 0 on ./dat/q4 9307 Testing fqzcomp_qual -r -s 1 on ./dat/q4 9618 Testing fqzcomp_qual -r -s 2 on ./dat/q4 9453 Testing fqzcomp_qual -r -s 3 on ./dat/q4 10481 Testing fqzcomp_qual -r -s 0 on ./dat/q40+dir 47674 Testing fqzcomp_qual -r -s 1 on ./dat/q40+dir 45016 Testing fqzcomp_qual -r -s 2 on ./dat/q40+dir 47760 Testing fqzcomp_qual -r -s 3 on ./dat/q40+dir 48583 Testing fqzcomp_qual -r -s 0 on ./dat/q8 30012 Testing fqzcomp_qual -r -s 1 on ./dat/q8 33742 Testing fqzcomp_qual -r -s 2 on ./dat/q8 30982 Testing fqzcomp_qual -r -s 3 on ./dat/q8 31709 Testing fqzcomp_qual -r -s 0 on ./dat/qvar 32868 Testing fqzcomp_qual -r -s 1 on ./dat/qvar 35007 Testing fqzcomp_qual -r -s 2 on ./dat/qvar 32400 Testing fqzcomp_qual -r -s 3 on ./dat/qvar 32073 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fvisibility=hidden -I. -Ihtscodecs -D_POSIX_C_SOURCE=200112L -c -o htscodecs/tests/varint_test.o htscodecs/tests/varint_test.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -fvisibility=hidden -rdynamic -o htscodecs/tests/varint htscodecs/tests/varint_test.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o -llzma -lbz2 -lz -lm -lm -lpthread cd htscodecs/tests && ./varint test/hts_endian test/test_expr test/test_kfunc test/test_kstring test/test_str2int test/fieldarith test/fieldarith.sam test/hfile HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" Expected error: [E::hts_parse_region] Unexpected string "x" after region Expected error: [E::hts_parse_region] Unexpected string "y" after region Expected error: [E::hts_parse_region] Unexpected string "chr3" after region cd test/sam_filter && ./filter.sh filter.tst Testing sam_filter... PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam |egrep -cv '^@' PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam |egrep -cv '^@' PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam |egrep -cv '^@' PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | egrep -cv '^@' PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | egrep -cv '^@' PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | egrep -cv '^@' PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | egrep -cv '^@' Expected passes: 14 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tabix && ./test-tabix.sh tabix.tst Testing tabix... PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 Expected passes: 14 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/mpileup && ./test-pileup.sh mpileup.tst Testing (m)pileup... PASS : $pileup mp_D.sam PASS : $pileup -m mp_D.sam PASS : $pileup mp_DI.sam PASS : $pileup -m mp_DI.sam PASS : $pileup mp_I.sam PASS : $pileup -m mp_I.sam PASS : $pileup mp_P.sam PASS : $pileup -m mp_P.sam PASS : $pileup mp_ID.sam PASS : $pileup -m mp_ID.sam PASS : $pileup mp_N.sam PASS : $pileup -m mp_N.sam PASS : $pileup mp_N2.sam PASS : $pileup -m mp_N2.sam PASS : $pileup c1#pad1.sam PASS : $pileup -m c1#pad1.sam PASS : $pileup c1#pad2.sam PASS : $pileup -m c1#pad2.sam PASS : $pileup c1#pad3.sam PASS : $pileup -m c1#pad3.sam PASS : $pileup -m small.bam Expected passes: 21 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/fastq && ./test-fastq.sh Testing fastq support PASS : $tview minimal.fq PASS : $tview minimal.fa PASS : $tview multiline.fq PASS : $tview multiline.fa PASS : $tview single.fq PASS : $tview single.fa PASS : $tview -i fastq_aux single.fq PASS : $tview -i fastq_aux single.fa PASS : $tview interleaved.fq PASS : $tview interleaved.fa PASS : $tview -i fastq_aux interleaved.fq PASS : $tview -i fastq_aux interleaved.fa PASS : $tview -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_casava filter_casava.fq PASS : $tview -i fastq_casava filter_casava.fa PASS : $tview -i fastq_aux r1.fq PASS : $tview -i fastq_aux r2.fq PASS : $tview -i fastq_aux r1.fa PASS : $tview -i fastq_aux r2.fa PASS : $tview -i fastq_name2 name2.fq PASS : $tview -i fastq_name2 name2.fa PASS : $tview -f minimal.sam PASS : $tview -F minimal.sam PASS : $tview -f -o fastq_aux single_aux.sam PASS : $tview -F -o fastq_aux single_aux.sam PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -f -o fastq_casava inter_casava.sam PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -F -o fastq_casava inter_casava.sam PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -f -o fastq_casava filter_casava.sam PASS : $tview -F -o fastq_casava filter_casava.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam Expected passes: 40 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/base_mods && ./base-mods.sh base-mods.tst Testing base-modifications... PASS : $test_mod MM-chebi.sam PASS : $test_mod MM-double.sam PASS : $test_mod MM-multi.sam PASS : $pileup_mod < MM-pileup.sam PASS : $pileup_mod < MM-pileup2.sam Expected passes: 5 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx.fa test/fastqs.fq (Expect trailing 'x' message for " -1,001x") [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] (Expect trailing 'k' message for "1.5e+3k") [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] (Expect dropped fraction message for "12.3456k") [W::hts_parse_decimal] Discarding fractional part of 12.3456k [W::hts_parse_decimal] Discarding fractional part of 12.3456k (Expect invalid numeric message for "A") [W::hts_parse_decimal] Invalid numeric value A[truncated] (Expect invalid numeric message for "G") [W::hts_parse_decimal] Invalid numeric value G[truncated] (Expect invalid numeric message for " +/-") [W::hts_parse_decimal] Invalid numeric value +/-[truncated] (Expect invalid numeric message for " -.e+9999") [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] test/test-regidx cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} "my" variable @p masks earlier declaration in same scope at ./test.pl line 617. bgzip round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/AOGzLp4yFi/index.bam.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/AOGzLp4yFi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/AOGzLp4yFi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -b -m 0 -x /tmp/AOGzLp4yFi/index.bam.bai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/AOGzLp4yFi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -b /tmp/AOGzLp4yFi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/AOGzLp4yFi/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/AOGzLp4yFi/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -b /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/AOGzLp4yFi/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index_dos.sam > /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/AOGzLp4yFi/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index_dos.sam > /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -b /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -C -x /tmp/AOGzLp4yFi/index.cram.crai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/AOGzLp4yFi/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index /tmp/AOGzLp4yFi/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -b -m 14 -x /tmp/AOGzLp4yFi/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.vcf > /tmp/AOGzLp4yFi/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/AOGzLp4yFi/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -z -m 14 -x /tmp/AOGzLp4yFi/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.vcf > /tmp/AOGzLp4yFi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/AOGzLp4yFi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -l 0 -z -m 0 -x /tmp/AOGzLp4yFi/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.vcf > /tmp/AOGzLp4yFi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -t /tmp/AOGzLp4yFi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/tabix /tmp/AOGzLp4yFi/index.vcf.gz##idx##/tmp/AOGzLp4yFi/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/AOGzLp4yFi/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/AOGzLp4yFi/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/AOGzLp4yFi/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/AOGzLp4yFi/index2.bam 2:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/AOGzLp4yFi/index.bam.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/AOGzLp4yFi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/AOGzLp4yFi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 0 -x /tmp/AOGzLp4yFi/index.bam.bai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/AOGzLp4yFi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -b /tmp/AOGzLp4yFi/index.bam .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/AOGzLp4yFi/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/AOGzLp4yFi/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -b /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/AOGzLp4yFi/index.sam.gz.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index_dos.sam > /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/AOGzLp4yFi/index.sam.gz.bai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index_dos.sam > /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -b /tmp/AOGzLp4yFi/index.sam.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -C -x /tmp/AOGzLp4yFi/index.cram.crai /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.sam > /tmp/AOGzLp4yFi/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index /tmp/AOGzLp4yFi/index.cram .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -b -m 14 -x /tmp/AOGzLp4yFi/index.bcf.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.vcf > /tmp/AOGzLp4yFi/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/AOGzLp4yFi/index.bcf .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 14 -x /tmp/AOGzLp4yFi/index.vcf.gz.csi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.vcf > /tmp/AOGzLp4yFi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c /tmp/AOGzLp4yFi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -@4 -l 0 -z -m 0 -x /tmp/AOGzLp4yFi/index.vcf.gz.tbi /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/index.vcf > /tmp/AOGzLp4yFi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -t /tmp/AOGzLp4yFi/index.vcf.gz .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/tabix /tmp/AOGzLp4yFi/index.vcf.gz##idx##/tmp/AOGzLp4yFi/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/AOGzLp4yFi/index2.bam 1:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/AOGzLp4yFi/index2.bam 1:2000000-2000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/AOGzLp4yFi/index2.bam 2:1000000-1000000 .. ok test_index: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /tmp/AOGzLp4yFi/index2.bam 2:2000000-2000000 .. ok test_view testing multi-ref CRAM modes: ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing multi-ref CRAM modes: ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing region queries: ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out .. ok test_view testing BAM files with absent @SQ lines: ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing region queries: ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out .. ok test_view testing BAM files with absent @SQ lines: ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_MD testing xx#MD.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ Checking for MD/NM in xx#MD.sam ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_MD testing xx#MD2.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_vcf_api: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-vcf-api /tmp/AOGzLp4yFi/test-vcf-api.bcf [W::bcf_record_check] Bad BCF record at 1:1: No REF allele [E::bcf_index_build3] TBI indices for BCF files are not supported [E::idx_find_and_load] Could not retrieve index file for '/tmp/AOGzLp4yFi/test-vcf-api.bcf' .. ok test_bcf2vcf: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-vcf-sweep /tmp/AOGzLp4yFi/test-vcf-api.bcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/htsfile -ch /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/formatcols.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/noroundtrip.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/formatmissing.vcf .. ok test_vcf_various: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/htsfile -c /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/vcf_meta_meta.vcf .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/AOGzLp4yFi -s 1356113804 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/AOGzLp4yFi -s 83133709 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/AOGzLp4yFi -s 667902312 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/AOGzLp4yFi -s 399748411 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/AOGzLp4yFi -s 1621162359 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/AOGzLp4yFi -s 1064992 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/AOGzLp4yFi -s 1597329569 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/AOGzLp4yFi -s 768416385 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/AOGzLp4yFi -s 1268969719 .. ok test-bcf-sr: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-sr.pl -t /tmp/AOGzLp4yFi -s 497732850 .. ok test_command: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-bcf-translate - .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/AOGzLp4yFi/headernul0.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/AOGzLp4yFi/headernul1.bam .. ok test_convert_padded_header: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_view -t ce.fa -C /tmp/AOGzLp4yFi/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/bgzip -I /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/bgziptest.txt.tmp.gz.gzi -c -g /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/bgziptest.txt .. ok test-logging: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1 /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/with-shlib.sh /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/htsfile https://localhost:99999/invalid_port .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -e -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn01.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn01.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -e -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -r -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02-r.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -a -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02_exp.sam -o - .. ok test_realn: /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/test_realn -f /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02.fa -i /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/test/realn02_exp-a.sam -o - .. ok Number of tests: total .. 172 passed .. 172 failed .. 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: htslib-1.15.1-6.fc42.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.kyQUlq + umask 022 + cd /builddir/build/BUILD/htslib-1.15.1-build + cd htslib-1.15.1 + DOCDIR=/builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/doc/htslib + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/doc/htslib + cp -pr /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/NEWS /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/doc/htslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.tB8gEz + umask 022 + cd /builddir/build/BUILD/htslib-1.15.1-build + cd htslib-1.15.1 + LICENSEDIR=/builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/licenses/htslib + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/licenses/htslib + cp -pr /builddir/build/BUILD/htslib-1.15.1-build/htslib-1.15.1/LICENSE /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT/usr/share/licenses/htslib + RPM_EC=0 ++ jobs -p + exit 0 Provides: htslib = 1.15.1-6.fc42 htslib(aarch-64) = 1.15.1-6.fc42 libhts.so.3()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libcrypto.so.3()(64bit) libcrypto.so.3(OPENSSL_3.0.0)(64bit) libcurl.so.4()(64bit) libhts.so.3()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-devel-1.15.1-6.fc42.aarch64 Provides: htslib-devel = 1.15.1-6.fc42 htslib-devel(aarch-64) = 1.15.1-6.fc42 pkgconfig(htslib) = 1.15.1 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/pkg-config libhts.so.3()(64bit) Processing files: htslib-tools-1.15.1-6.fc42.aarch64 Provides: htslib-tools = 1.15.1-6.fc42 htslib-tools(aarch-64) = 1.15.1-6.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: htslib-debugsource-1.15.1-6.fc42.aarch64 Provides: htslib-debugsource = 1.15.1-6.fc42 htslib-debugsource(aarch-64) = 1.15.1-6.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: htslib-debuginfo-1.15.1-6.fc42.aarch64 Provides: debuginfo(build-id) = 5e96095f6f9b9fd885d569621a661690a2cc4282 debuginfo(build-id) = 7e43a5c3b6fb6746b53fa9d08181e403ed4a95dd debuginfo(build-id) = 935af728cb754971103859062d1e90ce9b2207a2 debuginfo(build-id) = e3098b9bfd76006aca27fff3e59f6795c7c55efb debuginfo(build-id) = fd87058635b787c32bde6d074524971b2e6676b2 htslib-debuginfo = 1.15.1-6.fc42 htslib-debuginfo(aarch-64) = 1.15.1-6.fc42 libhts.so.1.15.1-1.15.1-6.fc42.aarch64.debug()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(aarch-64) = 1.15.1-6.fc42 Processing files: htslib-tools-debuginfo-1.15.1-6.fc42.aarch64 Provides: debuginfo(build-id) = 4615b875913c23a00c8194dcb2934c6c9c503ce0 debuginfo(build-id) = 57faa095a239714253044b7c45939704fdfe3a0c debuginfo(build-id) = ca5a6b72a8e1a18ef6c2ff5f5dea3e0691b00985 htslib-tools-debuginfo = 1.15.1-6.fc42 htslib-tools-debuginfo(aarch-64) = 1.15.1-6.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: htslib-debugsource(aarch-64) = 1.15.1-6.fc42 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/htslib-1.15.1-build/BUILDROOT Wrote: /builddir/build/RPMS/htslib-devel-1.15.1-6.fc42.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-1.15.1-6.fc42.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-tools-1.15.1-6.fc42.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-debuginfo-1.15.1-6.fc42.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-debugsource-1.15.1-6.fc42.aarch64.rpm Wrote: /builddir/build/RPMS/htslib-tools-debuginfo-1.15.1-6.fc42.aarch64.rpm Child return code was: 0