Diff of the two buildlogs: -- --- b1/build.log 2025-11-11 17:55:42.063737294 +0000 +++ b2/build.log 2025-11-11 17:57:33.175864463 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Nov 11 05:52:58 -12 2025 -I: pbuilder-time-stamp: 1762883578 +I: Current time: Tue Dec 15 14:18:44 +14 2026 +I: pbuilder-time-stamp: 1797293924 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -24,52 +24,84 @@ dpkg-source: info: applying reproducible.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/939202/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/81351/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 15 00:18 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/81351/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/81351/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='7c756b5deee748bcb2dee7a7d2078fd3' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='939202' - PS1='# ' - PS2='> ' + INVOCATION_ID=c49207ea7d124168b8b704b36f167a13 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=81351 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.SbhbzaRz/pbuilderrc_TQi0 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.SbhbzaRz/b1 --logfile b1/build.log samtools_1.22.1-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.SbhbzaRz/pbuilderrc_OgR6 --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.SbhbzaRz/b2 --logfile b2/build.log samtools_1.22.1-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.12.48+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/939202/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/81351/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -226,7 +258,7 @@ Get: 97 http://deb.debian.org/debian forky/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 tabix amd64 1.22.1+ds2-1 [542 kB] -Fetched 33.4 MB in 3s (10.3 MB/s) +Fetched 33.4 MB in 1s (55.8 MB/s) Preconfiguring packages ... Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19862 files and directories currently installed.) @@ -637,7 +669,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/samtools-1.22.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../samtools_1.22.1-1_source.changes +I: user script /srv/workspace/pbuilder/81351/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/81351/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/samtools-1.22.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../samtools_1.22.1-1_source.changes dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.22.1-1 dpkg-buildpackage: info: source distribution unstable @@ -652,7 +688,7 @@ rm -f config.mk touch config.mk dh_auto_clean -- - make -j12 distclean + make -j16 distclean make[2]: Entering directory '/build/reproducible-path/samtools-1.22.1' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/consensus && rm -f *.bam *.bam.csi @@ -740,7 +776,7 @@ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" - make -j12 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" CPPFLAGS="\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro -Wl,-z,now" + make -j16 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" CPPFLAGS="\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/samtools-1.22.1' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c @@ -753,35 +789,35 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c -cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c cc1: warning: command-line option '-frelease' is valid for D but not for C +echo '#define SAMTOOLS_VERSION "1.22.1"' > version.h cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option '-frelease' is valid for D but not for C -echo '#define SAMTOOLS_VERSION "1.22.1"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h +cc1: warning: command-line option '-frelease' is valid for D but not for C echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h echo '#define SAMTOOLS_CFLAGS "-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c sed -i -e 's@/build/reproducible-path/samtools-1.22.1@«BUILDPATH»@g' version.h +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c cc1: warning: command-line option '-frelease' is valid for D but not for C @@ -790,35 +826,35 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c @@ -832,8 +868,8 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c cc1: warning: command-line option '-frelease' is valid for D but not for C +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c cc1: warning: command-line option '-frelease' is valid for D but not for C @@ -848,9 +884,9 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_checksum.o bam_checksum.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c @@ -866,11 +902,11 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c @@ -878,21 +914,21 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c -cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c cc1: warning: command-line option '-frelease' is valid for D but not for C +cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c cc1: warning: command-line option '-frelease' is valid for D but not for C -ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz +ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c @@ -902,3306 +938,11 @@ cc1: warning: command-line option '-frelease' is valid for D but not for C cc1: warning: command-line option '-frelease' is valid for D but not for C gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o bam_checksum.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread +gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread -gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/reproducible-path/samtools-1.22.1' make[1]: Leaving directory '/build/reproducible-path/samtools-1.22.1' - rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log - debian/rules override_dh_auto_test -make[1]: Entering directory '/build/reproducible-path/samtools-1.22.1' -dh_auto_test -- BGZIP=/usr/bin/bgzip - make -j12 test TESTSUITEFLAGS="-j12 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip -make[2]: Entering directory '/build/reproducible-path/samtools-1.22.1' -test/split/test_count_rg -test/split/test_expand_format_string -test/split/test_filter_header_rg -test/split/test_parse_args -REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-} -test_reference: - /build/reproducible-path/samtools-1.22.1/samtools reference test/reference/mpileup.1.tmp.cram -.. ok - -test_reference: - /build/reproducible-path/samtools-1.22.1/samtools reference -e test/reference/mpileup.1.tmp.cram -.. ok - -test_reference: - /build/reproducible-path/samtools-1.22.1/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram -.. ok - -test_reference: - /build/reproducible-path/samtools-1.22.1/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram -.. ok - -test_reference: - /build/reproducible-path/samtools-1.22.1/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram -.. ok - -test_reference: - /build/reproducible-path/samtools-1.22.1/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram -.. ok - -test_reference: - /build/reproducible-path/samtools-1.22.1/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram -.. ok - -test_reference: - /build/reproducible-path/samtools-1.22.1/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram -.. ok - -/usr/bin/bgzip -c -b 65272 -s 5 /tmp/EQ6JAxW1Jo/bgzip.dat.gz -.. ok - -/usr/bin/bgzip -c -b 979200 -s 6 /tmp/EQ6JAxW1Jo/bgzip.dat.gz -.. ok - -/usr/bin/bgzip -c -b 652804 -s 6 /tmp/EQ6JAxW1Jo/bgzip.dat.gz -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/EQ6JAxW1Jo/faidx.fa 3:11-13 | grep -v '^>' -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/EQ6JAxW1Jo/faidx.fa.gz 3:11-13 | grep -v '^>' -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/EQ6JAxW1Jo/faidx.fa 2:998-1003 | grep -v '^>' -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/EQ6JAxW1Jo/faidx.fa.gz 2:998-1003 | grep -v '^>' -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/EQ6JAxW1Jo/faidx.fa 1:100-104 | grep -v '^>' -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/EQ6JAxW1Jo/faidx.fa.gz 1:100-104 | grep -v '^>' -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/EQ6JAxW1Jo/faidx.fa 1:99998-100007 | grep -v '^>' -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools faidx /tmp/EQ6JAxW1Jo/faidx.fa.gz 1:99998-100007 | grep -v '^>' -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/EQ6JAxW1Jo/fqidx.fq 3:11-13 -.. ok - -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/EQ6JAxW1Jo/fqidx.fq.gz 3:11-13 -.. ok - -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/EQ6JAxW1Jo/fqidx.fq 2:998-1003 -.. ok - -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/EQ6JAxW1Jo/fqidx.fq.gz 2:998-1003 -.. ok - -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/EQ6JAxW1Jo/fqidx.fq 1:100-104 -.. ok - -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/EQ6JAxW1Jo/fqidx.fq.gz 1:100-104 -.. ok - -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/EQ6JAxW1Jo/fqidx.fq 1:99998-100007 -.. ok - -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools fqidx /tmp/EQ6JAxW1Jo/fqidx.fq.gz 1:99998-100007 -.. ok - -.. ok - -test_dict: - /build/reproducible-path/samtools-1.22.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /build/reproducible-path/samtools-1.22.1/test/dat/dict.fa -.. ok - -test_dict: - /build/reproducible-path/samtools-1.22.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/EQ6JAxW1Jo/dict.fa.gz -.. ok - -test_dict: - cat /build/reproducible-path/samtools-1.22.1/test/dat/dict.fa | /build/reproducible-path/samtools-1.22.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz -.. ok - -test_dict: - /build/reproducible-path/samtools-1.22.1/samtools dict -AH < /build/reproducible-path/samtools-1.22.1/test/dat/dict.alias.fa -.. ok - -test_dict: - /build/reproducible-path/samtools-1.22.1/samtools dict -H -l /build/reproducible-path/samtools-1.22.1/test/dat/dict.alt < /build/reproducible-path/samtools-1.22.1/test/dat/dict.alias.fa -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools view /tmp/EQ6JAxW1Jo/large_chrom.bam ref2 -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools view /tmp/EQ6JAxW1Jo/large_chrom.bam ref2:1-541556283 -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools index /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam.bai -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools view -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/EQ6JAxW1Jo/test_input_1_b.bam.bai ref2 -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools view -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/EQ6JAxW1Jo/test_input_1_b.bam.bai -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam.bai /tmp/EQ6JAxW1Jo/test_input_1_b.bam.bai -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools view -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/EQ6JAxW1Jo/test_input_1_b_opt.bam.bai ref2 -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools index /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools index -M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam.bai -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools view -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam.bai ref2 -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools index -c /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam /tmp/EQ6JAxW1Jo/auto_indexed.csi && cat /tmp/EQ6JAxW1Jo/auto_indexed.csi -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools index /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.cram /tmp/EQ6JAxW1Jo/auto_indexed.crai && cat /tmp/EQ6JAxW1Jo/auto_indexed.crai -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools index -c /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.sam /tmp/EQ6JAxW1Jo/auto_indexed.csi && cat /tmp/EQ6JAxW1Jo/auto_indexed.csi -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools view -@ 2 /tmp/EQ6JAxW1Jo/large_chrom.bam ref2 -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools view -@ 2 /tmp/EQ6JAxW1Jo/large_chrom.bam ref2:1-541556283 -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools index -@ 2 /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam.bai -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools view -@ 2 -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/EQ6JAxW1Jo/test_input_1_b.bam.bai ref2 -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools view -@ 2 -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/EQ6JAxW1Jo/test_input_1_b.bam.bai -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam.bai /tmp/EQ6JAxW1Jo/test_input_1_b.bam.bai -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools view -@ 2 -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/EQ6JAxW1Jo/test_input_1_b_opt.bam.bai ref2 -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools index -@ 2 /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools index -@ 2 -M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam.bai -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools view -@ 2 -X /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam.bai ref2 -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools index -@ 2 -c /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam /tmp/EQ6JAxW1Jo/auto_indexed.csi && cat /tmp/EQ6JAxW1Jo/auto_indexed.csi -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools index -@ 2 /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.cram /tmp/EQ6JAxW1Jo/auto_indexed.crai && cat /tmp/EQ6JAxW1Jo/auto_indexed.crai -.. ok - -test_index: - /build/reproducible-path/samtools-1.22.1/samtools index -@ 2 -c /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.sam /tmp/EQ6JAxW1Jo/auto_indexed.csi && cat /tmp/EQ6JAxW1Jo/auto_indexed.csi -.. ok - -test_mpileup: - /build/reproducible-path/samtools-1.22.1/samtools mpileup -b /tmp/EQ6JAxW1Jo/mpileup.bam.list -f /tmp/EQ6JAxW1Jo/mpileup.ref.fa.gz -r17:100-150 -.. ok - -test_mpileup: - /build/reproducible-path/samtools-1.22.1/samtools mpileup -b /tmp/EQ6JAxW1Jo/mpileup.cram.list -f /tmp/EQ6JAxW1Jo/mpileup.ref.fa.gz -r17:100-150 -.. ok - -test_mpileup: - /build/reproducible-path/samtools-1.22.1/samtools mpileup -b /tmp/EQ6JAxW1Jo/mpileup.bam.urllist -f /tmp/EQ6JAxW1Jo/mpileup.ref.fa.gz -r17:100-150 -.. ok - -test_mpileup: - /build/reproducible-path/samtools-1.22.1/samtools mpileup -b /tmp/EQ6JAxW1Jo/mpileup.cram.urllist -f /tmp/EQ6JAxW1Jo/mpileup.ref.fa.gz -r17:100-150 -.. ok - -test_mpileup: - /build/reproducible-path/samtools-1.22.1/samtools mpileup -B --ff 0x14 -f /tmp/EQ6JAxW1Jo/mpileup.ref.fa.gz -r17:1050-1060 /tmp/EQ6JAxW1Jo/mpileup.1.bam | grep -v mpileup -.. ok - -test_mpileup: - /build/reproducible-path/samtools-1.22.1/samtools mpileup -B --ff 0x14 -f /tmp/EQ6JAxW1Jo/mpileup.ref.fa.gz -r17:1050-1060 /tmp/EQ6JAxW1Jo/mpileup.1.cram | grep -v mpileup -.. ok - -test_mpileup: - /build/reproducible-path/samtools-1.22.1/samtools mpileup /build/reproducible-path/samtools-1.22.1/test/mpileup/overlap.bam | grep 128814202 -.. ok - -test_usage: - samtools - samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, consensus, merge, mpileup, sort, split, quickcheck, fastq, fasta, import, reference, reset, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, checksum, flags, head, tview, view, depad, samples, help, version -.. ok - -test_usage_subcommand: - samtools dict - - Usage on stderr rather than stdout -.. expected failure - -test_usage_subcommand: - samtools faidx -.. ok - -test_usage_subcommand: - samtools fqidx -.. ok - -test_usage_subcommand: - samtools index -.. ok - -test_usage_subcommand: - samtools calmd - - Usage on stderr rather than stdout -.. expected failure - -test_usage_subcommand: - samtools fixmate -.. ok - -test_usage_subcommand: - samtools reheader - - Usage on stderr rather than stdout -.. expected failure - -test_usage_subcommand: - samtools targetcut - - Usage on stderr rather than stdout -.. expected failure - -test_usage_subcommand: - samtools addreplacerg -.. ok - -test_usage_subcommand: - samtools markdup - - Usage on stderr rather than stdout -.. expected failure - -test_usage_subcommand: - samtools ampliconclip - - Usage on stderr rather than stdout -.. expected failure - -test_usage_subcommand: - samtools collate -.. ok - -test_usage_subcommand: - samtools cat - - Usage on stderr rather than stdout -.. expected failure - -test_usage_subcommand: - samtools consensus -.. ok - -test_usage_subcommand: - samtools merge -.. ok - -test_usage_subcommand: - samtools mpileup - - Usage on stderr rather than stdout -.. expected failure - -test_usage_subcommand: - samtools sort -.. ok - -test_usage_subcommand: - samtools split -.. ok - -test_usage_subcommand: - samtools quickcheck -.. ok - -test_usage_subcommand: - samtools fastq -.. ok - -test_usage_subcommand: - samtools fasta -.. ok - -test_usage_subcommand: - samtools import -.. ok - -test_usage_subcommand: - samtools reference -.. ok - -test_usage_subcommand: - samtools reset -.. ok - -test_usage_subcommand: - samtools bedcov - - Usage on stderr rather than stdout -.. expected failure - -test_usage_subcommand: - samtools coverage -.. ok - -test_usage_subcommand: - samtools depth -.. ok - -test_usage_subcommand: - samtools flagstat -.. ok - -test_usage_subcommand: - samtools idxstats -.. ok - -test_usage_subcommand: - samtools phase - - Usage on stderr rather than stdout -.. expected failure - -test_usage_subcommand: - samtools stats -.. ok - -test_usage_subcommand: - samtools ampliconstats -.. ok - -test_usage_subcommand: - samtools checksum - - Usage on stderr rather than stdout -.. expected failure - -test_usage_subcommand: - samtools flags -.. ok - -test_usage_subcommand: - samtools head -.. ok - -test_usage_subcommand: - samtools tview - - Usage on stderr rather than stdout -.. expected failure - -test_usage_subcommand: - samtools view -.. ok - -test_usage_subcommand: - samtools depad - - Usage on stderr rather than stdout -.. expected failure - -test_usage_subcommand: - samtools samples - - Usage on stderr rather than stdout -.. expected failure - -test_view: - Generating test data file .................. done - 1: SAM -> BAM -> SAM .. ok - - 2: SAM -> uncompressed BAM .. ok - - 3: uncompressed BAM -> SAM and compare .. ok - - 4: SAM -> fast compressed BAM .. ok - - 5: fast compressed BAM -> SAM and compare .. ok - - 6: SAM -> CRAM -> SAM (UR header tags) .. ok - - 7: SAM -> CRAM -> SAM (M5 header tags) .. ok - - 8: BAM -> CRAM with UR -> SAM .. ok - - 9: SAM -> BAM (M5 header tags) .. ok - - 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok - - 11: CRAM -> BAM with UR .. ok - - 12: CRAM -> BAM with M5 .. ok - - 13: SAM -> SAM via stdout .. ok - - 14: SAM -> BAM via stdout .. ok - - 15: SAM -> CRAM via stdout .. ok - - 16: SAM from stdin -> SAM .. ok - - 17: BAM from stdin -> SAM .. ok - - 18: CRAM from stdin -> SAM .. ok - - 19: samtools view -H (SAM input) .. ok - - 20: samtools view -H (BAM input) .. ok - - 21: samtools view -H (CRAM input) .. ok - - 22: No headers (SAM input) .. ok - - 23: No headers (BAM input) .. ok - - 24: No headers (CRAM input) .. ok - - 25: Filter -f 128 (SAM input) .. ok - - 26: Count -f 128 (SAM input) .. ok - - 27: Filter -f 128 (BAM input) .. ok - - 28: Count -f 128 (BAM input) .. ok - - 29: Filter -f 128 (CRAM input) .. ok - - 30: Count -f 128 (CRAM input) .. ok - - 31: Filter -F 128 (SAM input) .. ok - - 32: Count -F 128 (SAM input) .. ok - - 33: Filter -F 128 (BAM input) .. ok - - 34: Count -F 128 (BAM input) .. ok - - 35: Filter -F 128 (CRAM input) .. ok - - 36: Count -F 128 (CRAM input) .. ok - - 37: Filter -F 128 -f 2 (SAM input) .. ok - - 38: Count -F 128 -f 2 (SAM input) .. ok - - 39: Filter -F 128 -f 2 (BAM input) .. ok - - 40: Count -F 128 -f 2 (BAM input) .. ok - - 41: Filter -F 128 -f 2 (CRAM input) .. ok - - 42: Count -F 128 -f 2 (CRAM input) .. ok - - 43: Filter -r grp2 (SAM input) .. ok - - 44: Count -r grp2 (SAM input) .. ok - - 45: Filter -r grp2 (BAM input) .. ok - - 46: Count -r grp2 (BAM input) .. ok - - 47: Filter -r grp2 (CRAM input) .. ok - - 48: Count -r grp2 (CRAM input) .. ok - - 49: Filter -R /tmp/EQ6JAxW1Jo/view.001.fogn (SAM input) .. ok - - 50: Count -R /tmp/EQ6JAxW1Jo/view.001.fogn (SAM input) .. ok - - 51: Filter -R /tmp/EQ6JAxW1Jo/view.001.fogn (BAM input) .. ok - - 52: Count -R /tmp/EQ6JAxW1Jo/view.001.fogn (BAM input) .. ok - - 53: Filter -R /tmp/EQ6JAxW1Jo/view.001.fogn (CRAM input) .. ok - - 54: Count -R /tmp/EQ6JAxW1Jo/view.001.fogn (CRAM input) .. ok - - 55: Filter -R /tmp/EQ6JAxW1Jo/view.001.fogn -r grp2 (SAM input).. ok - - 56: Count -R /tmp/EQ6JAxW1Jo/view.001.fogn -r grp2 (SAM input).. ok - - 57: Filter -R /tmp/EQ6JAxW1Jo/view.001.fogn -r grp2 (BAM input).. ok - - 58: Count -R /tmp/EQ6JAxW1Jo/view.001.fogn -r grp2 (BAM input).. ok - - 59: Filter -R /tmp/EQ6JAxW1Jo/view.001.fogn -r grp2 (CRAM input).. ok - - 60: Count -R /tmp/EQ6JAxW1Jo/view.001.fogn -r grp2 (CRAM input).. ok - - 61: Filter -r grp2 -R /tmp/EQ6JAxW1Jo/view.001.fogn (SAM input).. ok - - 62: Count -r grp2 -R /tmp/EQ6JAxW1Jo/view.001.fogn (SAM input).. ok - - 63: Filter -r grp2 -R /tmp/EQ6JAxW1Jo/view.001.fogn (BAM input).. ok - - 64: Count -r grp2 -R /tmp/EQ6JAxW1Jo/view.001.fogn (BAM input).. ok - - 65: Filter -r grp2 -R /tmp/EQ6JAxW1Jo/view.001.fogn (CRAM input).. ok - - 66: Count -r grp2 -R /tmp/EQ6JAxW1Jo/view.001.fogn (CRAM input).. ok - - 67: Filter -N /tmp/EQ6JAxW1Jo/view.001.forn (SAM input) .. ok - - 68: Count -N /tmp/EQ6JAxW1Jo/view.001.forn (SAM input) .. ok - - 69: Filter -N /tmp/EQ6JAxW1Jo/view.001.forn (BAM input) .. ok - - 70: Count -N /tmp/EQ6JAxW1Jo/view.001.forn (BAM input) .. ok - - 71: Filter -N /tmp/EQ6JAxW1Jo/view.001.forn (CRAM input) .. ok - - 72: Count -N /tmp/EQ6JAxW1Jo/view.001.forn (CRAM input) .. ok - - 73: Filter -d BC (SAM input) .. ok - - 74: Count -d BC (SAM input) .. ok - - 75: Filter -d BC (BAM input) .. ok - - 76: Count -d BC (BAM input) .. ok - - 77: Filter -d BC (CRAM input) .. ok - - 78: Count -d BC (CRAM input) .. ok - - 79: Filter -d BC:TGCA (SAM input) .. ok - - 80: Count -d BC:TGCA (SAM input) .. ok - - 81: Filter -d BC:TGCA (BAM input) .. ok - - 82: Count -d BC:TGCA (BAM input) .. ok - - 83: Filter -d BC:TGCA (CRAM input) .. ok - - 84: Count -d BC:TGCA (CRAM input) .. ok - - 85: Filter -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc (SAM input) .. ok - - 86: Count -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc (SAM input) .. ok - - 87: Filter -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc (BAM input) .. ok - - 88: Count -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc (BAM input) .. ok - - 89: Filter -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc (CRAM input) .. ok - - 90: Count -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc (CRAM input) .. ok - - 91: Filter -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc -d BC:TGCA (SAM input).. ok - - 92: Count -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc -d BC:TGCA (SAM input).. ok - - 93: Filter -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc -d BC:TGCA (BAM input).. ok - - 94: Count -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc -d BC:TGCA (BAM input).. ok - - 95: Filter -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc -d BC:TGCA (CRAM input).. ok - - 96: Count -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc -d BC:TGCA (CRAM input).. ok - - 97: Filter -d BC:TGCA -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc (SAM input).. ok - - 98: Count -d BC:TGCA -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc (SAM input).. ok - - 99: Filter -d BC:TGCA -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc (BAM input).. ok - - 100: Count -d BC:TGCA -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc (BAM input).. ok - - 101: Filter -d BC:TGCA -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc (CRAM input).. ok - - 102: Count -d BC:TGCA -D BC:/tmp/EQ6JAxW1Jo/view.001.fobc (CRAM input).. ok - - 103: Filter -D RG:/tmp/EQ6JAxW1Jo/view.001.fogn (SAM input) .. ok - - 104: Count -D RG:/tmp/EQ6JAxW1Jo/view.001.fogn (SAM input) .. ok - - 105: Filter -D RG:/tmp/EQ6JAxW1Jo/view.001.fogn (BAM input) .. ok - - 106: Count -D RG:/tmp/EQ6JAxW1Jo/view.001.fogn (BAM input) .. ok - - 107: Filter -D RG:/tmp/EQ6JAxW1Jo/view.001.fogn (CRAM input).. ok - - 108: Count -D RG:/tmp/EQ6JAxW1Jo/view.001.fogn (CRAM input) .. ok - - 109: Filter -d NE:TGCA (SAM input) .. ok - - 110: Count -d NE:TGCA (SAM input) .. ok - - 111: Filter -d NE:TGCA (BAM input) .. ok - - 112: Count -d NE:TGCA (BAM input) .. ok - - 113: Filter -d NE:TGCA (CRAM input) .. ok - - 114: Count -d NE:TGCA (CRAM input) .. ok - - 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -o /tmp/EQ6JAxW1Jo/view.test115.sam -h -d TGCA /tmp/EQ6JAxW1Jo/view.001.sam --no-PG - - -.. expected failure - - 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -c -d TGCA /tmp/EQ6JAxW1Jo/view.001.sam --no-PG - - -.. expected failure - - 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -o /tmp/EQ6JAxW1Jo/view.test117.sam -h -d TGCA /tmp/EQ6JAxW1Jo/view.test001.bam --no-PG - - -.. expected failure - - 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -c -d TGCA /tmp/EQ6JAxW1Jo/view.test001.bam --no-PG - - -.. expected failure - - 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -o /tmp/EQ6JAxW1Jo/view.test119.sam -h -d TGCA /tmp/EQ6JAxW1Jo/view.test006.cram --no-PG - - -.. expected failure - - 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -c -d TGCA /tmp/EQ6JAxW1Jo/view.test006.cram --no-PG - - -.. expected failure - - 121: Filter -D BClong:/tmp/EQ6JAxW1Jo/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/EQ6JAxW1Jo/view.001.fobc" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -o /tmp/EQ6JAxW1Jo/view.test121.sam -h -D BClong:/tmp/EQ6JAxW1Jo/view.001.fobc /tmp/EQ6JAxW1Jo/view.001.sam --no-PG - - -.. expected failure - - 122: Count -D BClong:/tmp/EQ6JAxW1Jo/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/EQ6JAxW1Jo/view.001.fobc" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -c -D BClong:/tmp/EQ6JAxW1Jo/view.001.fobc /tmp/EQ6JAxW1Jo/view.001.sam --no-PG - - -.. expected failure - - 123: Filter -D BClong:/tmp/EQ6JAxW1Jo/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/EQ6JAxW1Jo/view.001.fobc" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -o /tmp/EQ6JAxW1Jo/view.test123.sam -h -D BClong:/tmp/EQ6JAxW1Jo/view.001.fobc /tmp/EQ6JAxW1Jo/view.test001.bam --no-PG - - -.. expected failure - - 124: Count -D BClong:/tmp/EQ6JAxW1Jo/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/EQ6JAxW1Jo/view.001.fobc" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -c -D BClong:/tmp/EQ6JAxW1Jo/view.001.fobc /tmp/EQ6JAxW1Jo/view.test001.bam --no-PG - - -.. expected failure - - 125: Filter -D BClong:/tmp/EQ6JAxW1Jo/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/EQ6JAxW1Jo/view.001.fobc" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -o /tmp/EQ6JAxW1Jo/view.test125.sam -h -D BClong:/tmp/EQ6JAxW1Jo/view.001.fobc /tmp/EQ6JAxW1Jo/view.test006.cram --no-PG - - -.. expected failure - - 126: Count -D BClong:/tmp/EQ6JAxW1Jo/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/EQ6JAxW1Jo/view.001.fobc" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -c -D BClong:/tmp/EQ6JAxW1Jo/view.001.fobc /tmp/EQ6JAxW1Jo/view.test006.cram --no-PG - - -.. expected failure - - 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -o /tmp/EQ6JAxW1Jo/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/EQ6JAxW1Jo/view.001.sam --no-PG - - -.. expected failure - - 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/EQ6JAxW1Jo/view.001.sam --no-PG - - -.. expected failure - - 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -o /tmp/EQ6JAxW1Jo/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/EQ6JAxW1Jo/view.test001.bam --no-PG - - -.. expected failure - - 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/EQ6JAxW1Jo/view.test001.bam --no-PG - - -.. expected failure - - 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -o /tmp/EQ6JAxW1Jo/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/EQ6JAxW1Jo/view.test006.cram --no-PG - - -.. expected failure - - 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" - Failed command: - /build/reproducible-path/samtools-1.22.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/EQ6JAxW1Jo/view.test006.cram --no-PG - - -.. expected failure - - 133: Filter -d NM:13 (SAM input) .. ok - - 134: Count -d NM:13 (SAM input) .. ok - - 135: Filter -d NM:13 (BAM input) .. ok - - 136: Count -d NM:13 (BAM input) .. ok - - 137: Filter -d NM:13 (CRAM input) .. ok - - 138: Count -d NM:13 (CRAM input) .. ok - - 139: Filter -d ab:z (SAM input) .. ok - - 140: Count -d ab:z (SAM input) .. ok - - 141: Filter -d ab:z (BAM input) .. ok - - 142: Count -d ab:z (BAM input) .. ok - - 143: Filter -d ab:z (CRAM input) .. ok - - 144: Count -d ab:z (CRAM input) .. ok - - 145: Filter -l Library 2 (SAM input) .. ok - - 146: Count -l Library 2 (SAM input) .. ok - - 147: Filter -l Library 2 (BAM input) .. ok - - 148: Count -l Library 2 (BAM input) .. ok - - 149: Filter -l Library 2 (CRAM input) .. ok - - 150: Count -l Library 2 (CRAM input) .. ok - - 151: Filter -l Library 3 (SAM input) .. ok - - 152: Count -l Library 3 (SAM input) .. ok - - 153: Filter -l Library 3 (BAM input) .. ok - - 154: Count -l Library 3 (BAM input) .. ok - - 155: Filter -l Library 3 (CRAM input) .. ok - - 156: Count -l Library 3 (CRAM input) .. ok - - 157: Filter -q 50 (SAM input) .. ok - - 158: Count -q 50 (SAM input) .. ok - - 159: Filter -q 50 (BAM input) .. ok - - 160: Count -q 50 (BAM input) .. ok - - 161: Filter -q 50 (CRAM input) .. ok - - 162: Count -q 50 (CRAM input) .. ok - - 163: Filter -q 99 (SAM input) .. ok - - 164: Count -q 99 (SAM input) .. ok - - 165: Filter -q 99 (BAM input) .. ok - - 166: Count -q 99 (BAM input) .. ok - - 167: Filter -q 99 (CRAM input) .. ok - - 168: Count -q 99 (CRAM input) .. ok - - 169: Filter -q 100 (SAM input) .. ok - - 170: Count -q 100 (SAM input) .. ok - - 171: Filter -q 100 (BAM input) .. ok - - 172: Count -q 100 (BAM input) .. ok - - 173: Filter -q 100 (CRAM input) .. ok - - 174: Count -q 100 (CRAM input) .. ok - - 175: Filter -x fa (SAM input) .. ok - - 176: Count -x fa (SAM input) .. ok - - 177: Filter -x fa (BAM input) .. ok - - 178: Count -x fa (BAM input) .. ok - - 179: Filter -x fa (CRAM input) .. ok - - 180: Count -x fa (CRAM input) .. ok - - 181: Filter -x fa -x ha (SAM input) .. ok - - 182: Count -x fa -x ha (SAM input) .. ok - - 183: Filter -x fa -x ha (BAM input) .. ok - - 184: Count -x fa -x ha (BAM input) .. ok - - 185: Filter -x fa -x ha (CRAM input) .. ok - - 186: Count -x fa -x ha (CRAM input) .. ok - - 187: Filter -x fa,ha (SAM input) .. ok - - 188: Count -x fa,ha (SAM input) .. ok - - 189: Filter -x fa,ha (BAM input) .. ok - - 190: Count -x fa,ha (BAM input) .. ok - - 191: Filter -x fa,ha (CRAM input) .. ok - - 192: Count -x fa,ha (CRAM input) .. ok - - 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok - - 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok - - 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok - - 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok - - 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok - - 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok - - 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok - - 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok - - 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok - - 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok - - 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok - - 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok - - 205: Filter -x fa -r grp2 (SAM input) .. ok - - 206: Count -x fa -r grp2 (SAM input) .. ok - - 207: Filter -x fa -r grp2 (BAM input) .. ok - - 208: Count -x fa -r grp2 (BAM input) .. ok - - 209: Filter -x fa -r grp2 (CRAM input) .. ok - - 210: Count -x fa -r grp2 (CRAM input) .. ok - - 211: Filter -x RG -r grp2 (SAM input) .. ok - - 212: Count -x RG -r grp2 (SAM input) .. ok - - 213: Filter -x RG -r grp2 (BAM input) .. ok - - 214: Count -x RG -r grp2 (BAM input) .. ok - - 215: Filter -x RG -r grp2 (CRAM input) .. ok - - 216: Count -x RG -r grp2 (CRAM input) .. ok - - 217: Filter -m 10 (SAM input) .. ok - - 218: Count -m 10 (SAM input) .. ok - - 219: Filter -m 10 (BAM input) .. ok - - 220: Count -m 10 (BAM input) .. ok - - 221: Filter -m 10 (CRAM input) .. ok - - 222: Count -m 10 (CRAM input) .. ok - - 223: Filter -m 11 (SAM input) .. ok - - 224: Count -m 11 (SAM input) .. ok - - 225: Filter -m 11 (BAM input) .. ok - - 226: Count -m 11 (BAM input) .. ok - - 227: Filter -m 11 (CRAM input) .. ok - - 228: Count -m 11 (CRAM input) .. ok - - 229: Filter -m 15 (SAM input) .. ok - - 230: Count -m 15 (SAM input) .. ok - - 231: Filter -m 15 (BAM input) .. ok - - 232: Count -m 15 (BAM input) .. ok - - 233: Filter -m 15 (CRAM input) .. ok - - 234: Count -m 15 (CRAM input) .. ok - - 235: Filter -m 16 (SAM input) .. ok - - 236: Count -m 16 (SAM input) .. ok - - 237: Filter -m 16 (BAM input) .. ok - - 238: Count -m 16 (BAM input) .. ok - - 239: Filter -m 16 (CRAM input) .. ok - - 240: Count -m 16 (CRAM input) .. ok - - 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok - - 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok - - 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok - - 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok - - 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok - - 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok - - 247: Filter -e [BC] (SAM input) .. ok - - 248: Count -e [BC] (SAM input) .. ok - - 249: Filter -e [BC] (BAM input) .. ok - - 250: Count -e [BC] (BAM input) .. ok - - 251: Filter -e [BC] (CRAM input) .. ok - - 252: Count -e [BC] (CRAM input) .. ok - - 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok - - 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok - - 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok - - 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok - - 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok - - 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok - - 259: Filter -e mapq >= 50 (SAM input) .. ok - - 260: Count -e mapq >= 50 (SAM input) .. ok - - 261: Filter -e mapq >= 50 (BAM input) .. ok - - 262: Count -e mapq >= 50 (BAM input) .. ok - - 263: Filter -e mapq >= 50 (CRAM input) .. ok - - 264: Count -e mapq >= 50 (CRAM input) .. ok - - 265: Filter -e mapq >= 99 (SAM input) .. ok - - 266: Count -e mapq >= 99 (SAM input) .. ok - - 267: Filter -e mapq >= 99 (BAM input) .. ok - - 268: Count -e mapq >= 99 (BAM input) .. ok - - 269: Filter -e mapq >= 99 (CRAM input) .. ok - - 270: Count -e mapq >= 99 (CRAM input) .. ok - - 271: Filter -e mapq >= 100 (SAM input) .. ok - - 272: Count -e mapq >= 100 (SAM input) .. ok - - 273: Filter -e mapq >= 100 (BAM input) .. ok - - 274: Count -e mapq >= 100 (BAM input) .. ok - - 275: Filter -e mapq >= 100 (CRAM input) .. ok - - 276: Count -e mapq >= 100 (CRAM input) .. ok - - 277: 1bp reads file SAM -> BAM -> SAM .. ok - - 278: 1bp reads file SAM -> CRAM -> SAM .. ok - - 278: Region Z (BAM input) .. ok - - 279: Count Z (BAM input) .. ok - - 280: Region Z (CRAM input) .. ok - - 281: Count Z (CRAM input) .. ok - - 282: Region Z:30 (BAM input) .. ok - - 283: Count Z:30 (BAM input) .. ok - - 284: Region Z:30 (CRAM input) .. ok - - 285: Count Z:30 (CRAM input) .. ok - - 286: Region Z:20-40 (BAM input) .. ok - - 287: Count Z:20-40 (BAM input) .. ok - - 288: Region Z:20-40 (CRAM input) .. ok - - 289: Count Z:20-40 (CRAM input) .. ok - - 290: Region ref1 (BAM input) .. ok - - 291: Count ref1 (BAM input) .. ok - - 292: Region ref1 (CRAM input) .. ok - - 293: Count ref1 (CRAM input) .. ok - - 294: Region ref1:15 (BAM input) .. ok - - 295: Count ref1:15 (BAM input) .. ok - - 296: Region ref1:15 (CRAM input) .. ok - - 297: Count ref1:15 (CRAM input) .. ok - - 298: Region ref1:15-45 (BAM input) .. ok - - 299: Count ref1:15-45 (BAM input) .. ok - - 300: Region ref1:15-45 (CRAM input) .. ok - - 301: Count ref1:15-45 (CRAM input) .. ok - - 302: Region ref1:15-45 ref2 (BAM input) .. ok - - 303: Count ref1:15-45 ref2 (BAM input) .. ok - - 304: Region ref1:15-45 ref2 (CRAM input) .. ok - - 305: Count ref1:15-45 ref2 (CRAM input) .. ok - - 306: Region ref1:15-45 ref2:16 (BAM input) .. ok - - 307: Count ref1:15-45 ref2:16 (BAM input) .. ok - - 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok - - 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok - - 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok - - 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok - - 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok - - 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok - - 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok - - 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok - - 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok - - 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok - - 318: Region -f 128 ref1 (BAM input) .. ok - - 319: Count -f 128 ref1 (BAM input) .. ok - - 320: Region -f 128 ref1 (CRAM input) .. ok - - 321: Count -f 128 ref1 (CRAM input) .. ok - - 322: Region -q 50 ref1:15-45 (BAM input) .. ok - - 323: Count -q 50 ref1:15-45 (BAM input) .. ok - - 324: Region -q 50 ref1:15-45 (CRAM input) .. ok - - 325: Count -q 50 ref1:15-45 (CRAM input) .. ok - - 326: Region -r grp2 ref1:15-45 (BAM input) .. ok - - 327: Count -r grp2 ref1:15-45 (BAM input) .. ok - - 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok - - 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok - - 330: Region * (BAM input) .. ok - - 331: Count * (BAM input) .. ok - - 332: Region * (CRAM input) .. ok - - 333: Count * (CRAM input) .. ok - - 334: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed (BAM input).. ok - - 335: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed (BAM input).. ok - - 336: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed (CRAM input).. ok - - 337: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed (CRAM input).. ok - - 338: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.02.bed (BAM input).. ok - - 339: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.02.bed (BAM input).. ok - - 340: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.02.bed (CRAM input).. ok - - 341: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.02.bed (CRAM input).. ok - - 342: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed (BAM input).. ok - - 343: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed (BAM input).. ok - - 344: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed (CRAM input).. ok - - 345: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed (CRAM input).. ok - - 346: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.02.bed (BAM input).. ok - - 347: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.02.bed (BAM input).. ok - - 348: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.02.bed (CRAM input).. ok - - 349: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.02.bed (CRAM input).. ok - - 350: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.03.bed (BAM input).. ok - - 351: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.03.bed (BAM input).. ok - - 352: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.03.bed (CRAM input).. ok - - 353: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.03.bed (CRAM input).. ok - - 354: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z (BAM input).. ok - - 355: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z (BAM input).. ok - - 356: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z (CRAM input).. ok - - 357: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z (CRAM input).. ok - - 358: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok - - 359: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok - - 360: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok - - 361: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok - - 362: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok - - 363: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok - - 364: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok - - 365: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok - - 366: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok - - 367: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok - - 368: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok - - 369: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok - - 370: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok - - 371: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok - - 372: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok - - 373: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok - - 374: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref2 (BAM input).. ok - - 375: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref2 (BAM input).. ok - - 376: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok - - 377: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok - - 378: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok - - 379: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok - - 380: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok - - 381: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok - - 382: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok - - 383: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok - - 384: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok - - 385: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok - - 386: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok - - 387: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok - - 388: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok - - 389: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok - - 390: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok - - 391: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok - - 392: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok - - 393: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok - - 394: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok - - 395: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok - - 396: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok - - 397: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok - - 398: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok - - 399: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok - - 400: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok - - 401: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok - - 402: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok - - 403: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok - - 404: Region -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok - - 405: Count -L /build/reproducible-path/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok - - 406: -L with nested regions .. ok - - 407: Make BAM with no M5/UR tags .. ok - - 408: Add @SQ with -t (SAM -> SAM) .. ok - - 409: Add @SQ with -T (SAM -> SAM) .. ok - - 410: Add @SQ with -t (BAM -> SAM) .. ok - - 411: Add @SQ with -T (BAM -> SAM) .. ok - - 412: Add @SQ with -t (SAM -> BAM) .. ok - - 413: Add @SQ with -T (SAM -> BAM) .. ok - - 414: Add @SQ with -t (BAM -> BAM) .. ok - - 415: Add @SQ with -T (BAM -> BAM) .. ok - - 416: Add @SQ with -t (SAM -> CRAM) .. ok - - 417: Add @SQ with -T (SAM -> CRAM) .. ok - - 418: Add @SQ with -t (BAM -> CRAM) .. ok - - 419: Add @SQ with -T (BAM -> CRAM) .. ok - - 420: Make CRAM with no UR field .. ok - - 421: Decoding CRAM with no UR field via -T .. ok - - 422: CIGAR B-operator removal .. ok - - 423: Big SAM -> BAM .. ok - - 424: Big SAM -> BAM (2 threads) .. ok - - 425: Big SAM -> BAM (4 threads) .. ok - - 426: Big SAM -> CRAM .. ok - - 427: Big SAM -> CRAM (2 threads) .. ok - - 428: Big SAM -> CRAM (4 threads) .. ok - - 429: Subsample 0.2 (SAM input) ............ ok - - 430: Subsample 0.5 (SAM input) ............ ok - - 431: Subsample 0.8 (SAM input) ............ ok - - 432: Subsample 0.2 (BAM input) ............ ok - - 433: Subsample 0.5 (BAM input) ............ ok - - 434: Subsample 0.8 (BAM input) ............ ok - - 435: Subsample 0.2 (CRAM input) ............ ok - - 436: Subsample 0.5 (CRAM input) ............ ok - - 437: Subsample 0.8 (CRAM input) ............ ok - - 438: SAM add PG .. ok - - 439: Unset dup flag, remove dt and do tags .. ok - - 440: Unmap dup flagged reads. .. ok - - 441: Unmap dup flagged reads. .. ok - - 442: fetch pairs .. ok - - 443: fetch pairs .. ok - - 444: fetch pairs .. ok - -test_head: - /build/reproducible-path/samtools-1.22.1/samtools head /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam -.. ok - -test_head: - /build/reproducible-path/samtools-1.22.1/samtools head -h 0 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam -.. ok - -test_head: - /build/reproducible-path/samtools-1.22.1/samtools head -h 1 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam -.. ok - -test_head: - /build/reproducible-path/samtools-1.22.1/samtools head -h 5 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam -.. ok - -test_head: - /build/reproducible-path/samtools-1.22.1/samtools head -h 29 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam -.. ok - -test_head: - /build/reproducible-path/samtools-1.22.1/samtools head -h 30 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam -.. ok - -test_head: - /build/reproducible-path/samtools-1.22.1/samtools head -n 0 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam -.. ok - -test_head: - /build/reproducible-path/samtools-1.22.1/samtools head -n 1 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam -.. ok - -test_head: - /build/reproducible-path/samtools-1.22.1/samtools head -n 5 /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam -.. ok - -test_head: - /build/reproducible-path/samtools-1.22.1/samtools head -h 5 -n 5 < /build/reproducible-path/samtools-1.22.1/test/dat/view.001.sam -.. ok - -test_cat: - Generating test data file .................. done - Generate BAM file #1 .. ok - - Generate BAM region file #1 .. ok - - Generate CRAM file #1 .. ok - - Generating test data file .................. done - Generate BAM file #2 .. ok - - Generate BAM region file #2 .. ok - - Generate CRAM file #2 .. ok - - Generating test data file .................. done - Generate BAM file #3 .. ok - - Generate BAM region file #3 .. ok - - Generate CRAM file #3 .. ok - - Generating test data file .................. done - Generate BAM file #4 .. ok - - Generate BAM region file #4 .. ok - - Generate CRAM file #4 .. ok - - 1: cat BAM files .. ok - - 2: cat recompressed BAM files .. ok - - 3: cat CRAM files .. ok - - 4: cat CRAM subregion files .. ok - - 5: cat BAM files to stdout .. ok - - 6: cat recompressed BAM files to stdout .. ok - - 7: cat CRAM files to stdout .. ok - - 8: cat CRAM subregion files to stdout .. ok - - 9: cat CRAM part 1/2 .. ok - - 9: cat CRAM part 2/2 .. ok - - 9: cat CRAM parts 1/2 + 2/2 .. ok - - 10: cat BAM files with new header .. ok - - 11: cat recompressed BAM files with new header .. ok - - 12: cat CRAM files with new header .. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -0 /build/reproducible-path/samtools-1.22.1/test/0.fq -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -0 /build/reproducible-path/samtools-1.22.1/test/0.fq -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -N -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -N -T RG,BC,QT -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /build/reproducible-path/samtools-1.22.1/samtools fastq -N -T RG,BC,QT,MD,ia -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/import/2.interleaved.fq -T "" -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/import/3.interleaved.fq -i -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/import/4.aux.fq -T "*" -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/import/4.aux.fq -T "" -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq -.. ok - -test_import: - /build/reproducible-path/samtools-1.22.1/samtools import --no-PG --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ -.. ok - -test_bam2fq: - Generate BAM file .. ok - - Generate CRAM file .. ok - - 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons -[M::bam2fq_mainloop] processed 36 reads -.. ok - - 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons -[M::bam2fq_mainloop] processed 36 reads -.. ok - - 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons -[M::bam2fq_mainloop] processed 36 reads -.. ok - - 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons -[M::bam2fq_mainloop] processed 36 reads -.. ok - - 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons -[M::bam2fq_mainloop] processed 36 reads -.. ok - - 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons -[M::bam2fq_mainloop] processed 36 reads -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.002.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.003.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/bc.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.004.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/bc.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.004.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/bc.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.010.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.22.1/test/bc_split.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -N -t -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -N -t -T MD,ia -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/i.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.004.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.22.1/test/i.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.703.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -N -1 /build/reproducible-path/samtools-1.22.1/test/o.fq -2 /build/reproducible-path/samtools-1.22.1/test/o.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fasta -N -1 /build/reproducible-path/samtools-1.22.1/test/o.fa -2 /build/reproducible-path/samtools-1.22.1/test/o.fa /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -N -o /build/reproducible-path/samtools-1.22.1/test/o.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -N -s /tmp/EQ6JAxW1Jo/bam2fq.discard.s.fq -0 /tmp/EQ6JAxW1Jo/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.013.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.22.1/test/i1.fq --i2 /build/reproducible-path/samtools-1.22.1/test/i2.fq -0 /build/reproducible-path/samtools-1.22.1/test/0.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.014.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -N -T '' /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -N -t -T '*' /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -N -T '*' -d ia /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - Generate BAM file (2 threads) .. ok - - Generate CRAM file (2 threads) .. ok - - 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons -[M::bam2fq_mainloop] processed 36 reads -.. ok - - 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons -[M::bam2fq_mainloop] processed 36 reads -.. ok - - 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons -[M::bam2fq_mainloop] processed 36 reads -.. ok - - 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons -[M::bam2fq_mainloop] processed 36 reads -.. ok - - 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons -[M::bam2fq_mainloop] processed 36 reads -.. ok - - 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons -[M::bam2fq_mainloop] processed 36 reads -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.002.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.003.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/bc.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.004.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/bc.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.004.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/bc.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.010.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.22.1/test/bc_split.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -t -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -t -T MD,ia -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.22.1/test/i.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.004.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.22.1/test/i.fq -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.22.1/test/s.fq -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.005.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.22.1/test/1.fq -2 /build/reproducible-path/samtools-1.22.1/test/2.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.703.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -1 /build/reproducible-path/samtools-1.22.1/test/o.fq -2 /build/reproducible-path/samtools-1.22.1/test/o.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fasta -@ 2 -N -1 /build/reproducible-path/samtools-1.22.1/test/o.fa -2 /build/reproducible-path/samtools-1.22.1/test/o.fa /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -o /build/reproducible-path/samtools-1.22.1/test/o.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -s /tmp/EQ6JAxW1Jo/bam2fq.discard.s.fq -0 /tmp/EQ6JAxW1Jo/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.013.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.22.1/test/i1.fq --i2 /build/reproducible-path/samtools-1.22.1/test/i2.fq -0 /build/reproducible-path/samtools-1.22.1/test/0.fq /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.014.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -T '' /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -t -T '*' /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -N -T '*' -d ia /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_bam2fq: - /build/reproducible-path/samtools-1.22.1/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.22.1/test/dat/bam2fq.001.sam -.. ok - -test_depad: - Generate BAM file .. ok - - depad (SAM input) .. ok - - depad -s (SAM input) .. ok - - depad -u (SAM input) .. ok - - depad -1 (SAM input) .. ok - - depad (BAM input) .. ok - - depad -s (BAM input) .. ok - - depad -u (BAM input) .. ok - - depad -1 (BAM input) .. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/1_map_cigar.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/1_map_cigar_large.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/4_X_cigar_full_seq.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/5_insert_cigar.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/5_insert_cigar_large.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa -i 0 /build/reproducible-path/samtools-1.22.1/test/stat/5_insert_cigar.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/7_supp.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/7_supp_large.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/8_secondary.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/8_secondary_large.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -S RG -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/1_map_cigar.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -S RG -r /build/reproducible-path/samtools-1.22.1/test/stat/test.fa /build/reproducible-path/samtools-1.22.1/test/stat/10_map_cigar.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -t /build/reproducible-path/samtools-1.22.1/test/stat/11.stats.targets /build/reproducible-path/samtools-1.22.1/test/stat/11_target.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -g 4 -t /build/reproducible-path/samtools-1.22.1/test/stat/11.stats.targets /build/reproducible-path/samtools-1.22.1/test/stat/11_target.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -g 4 /build/reproducible-path/samtools-1.22.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.22.1/test/stat/12_3reads.bed | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.22.1/test/stat/12_3reads.bed | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.22.1/test/stat/12_2reads.bed | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.22.1/test/stat/12_2reads.bed | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/13_barcodes_ok.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 - - /build/reproducible-path/samtools-1.22.1/test/stat/13.barcodes.fail.expected: No such file or directory -.. expected failure - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 - - /build/reproducible-path/samtools-1.22.1/test/stat/13.barcodes.fail.expected: No such file or directory -.. expected failure - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats /build/reproducible-path/samtools-1.22.1/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 - - /build/reproducible-path/samtools-1.22.1/test/stat/13.barcodes.fail.expected: No such file or directory -.. expected failure - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -I s1 /build/reproducible-path/samtools-1.22.1/test/stat/11_target.bam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -I grp2 /build/reproducible-path/samtools-1.22.1/test/stat/11_target.bam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -I grp3 /build/reproducible-path/samtools-1.22.1/test/stat/11_target.bam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -I Sample /build/reproducible-path/samtools-1.22.1/test/stat/11_target.bam | tail -n+4 -.. ok - -test_stats: - /build/reproducible-path/samtools-1.22.1/samtools stats -r /build/reproducible-path/samtools-1.22.1/test/mpileup/ce.fa /build/reproducible-path/samtools-1.22.1/test/stat/15.big_del.sam | tail -n+4 -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.bam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -O sam -b /tmp/r7utX_dd3q - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -r -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -cp -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b_regex.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -o - -s 1 -O sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/EQ6JAxW1Jo/merge.tag.1.bam /tmp/EQ6JAxW1Jo/merge.tag.2.bam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/EQ6JAxW1Jo/merge.tag.3.bam /tmp/EQ6JAxW1Jo/merge.tag.4.bam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge --no-PG -O SAM - /build/reproducible-path/samtools-1.22.1/test/merge/test_no_pg_rg_co.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.22.1/test/merge/merge.bed - /tmp/EQ6JAxW1Jo/merge.bed.1.bam /tmp/EQ6JAxW1Jo/merge.bed.2.bam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge --no-PG -r -O SAM - /build/reproducible-path/samtools-1.22.1/test/merge/test_no_pg_rg_co.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge --no-PG -O SAM --template-coordinate - /build/reproducible-path/samtools-1.22.1/test/merge/test_template_coordinate.1.sam /build/reproducible-path/samtools-1.22.1/test/merge/test_template_coordinate.2.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.bam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/MHDG7TeuCI - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -r -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -cp -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b_regex.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -o - -s 1 -O sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_c.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/EQ6JAxW1Jo/merge.tag.1.bam /tmp/EQ6JAxW1Jo/merge.tag.2.bam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/EQ6JAxW1Jo/merge.tag.3.bam /tmp/EQ6JAxW1Jo/merge.tag.4.bam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 --no-PG -O SAM - /build/reproducible-path/samtools-1.22.1/test/merge/test_no_pg_rg_co.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.22.1/test/merge/merge.bed - /tmp/EQ6JAxW1Jo/merge.bed.1.bam /tmp/EQ6JAxW1Jo/merge.bed.2.bam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 --no-PG -r -O SAM - /build/reproducible-path/samtools-1.22.1/test/merge/test_no_pg_rg_co.sam -.. ok - -test_merge: - /build/reproducible-path/samtools-1.22.1/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /build/reproducible-path/samtools-1.22.1/test/merge/test_template_coordinate.1.sam /build/reproducible-path/samtools-1.22.1/test/merge/test_template_coordinate.2.sam -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/EQ6JAxW1Jo/sortout -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -f /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/EQ6JAxW1Jo/sortout.bam -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -o /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/EQ6JAxW1Jo/sorttmp -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -n -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -N -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -n -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/sort_name_input_1.sam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -t RG -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -n -t RG -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -t AS -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -t FI -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort --template-coordinate -m 10M /build/reproducible-path/samtools-1.22.1/test/sort/template-coordinate.sort.sam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools sort -m 10M -M -K10 -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools sort -m 10M -M -K10 -I /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.ref.fa -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools sort -m 10M -MH -K10 -I /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.ref.fa -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/EQ6JAxW1Jo/sortout -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/EQ6JAxW1Jo/sortout.bam -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/EQ6JAxW1Jo/sorttmp -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -N -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_b.bam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/sort_name_input_1.sam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -t RG -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -n -t RG -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -t AS -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -t FI -m 10M /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 --template-coordinate -m 10M /build/reproducible-path/samtools-1.22.1/test/sort/template-coordinate.sort.sam -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -m 10M -M -K10 -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -m 10M -M -K10 -I /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.ref.fa -O SAM -o - -.. ok - -test_sort: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools sort -@ 2 -m 10M -MH -K10 -I /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.ref.fa -O SAM -o - -.. ok - -test_collate: - /build/reproducible-path/samtools-1.22.1/samtools collate --output-fmt=sam -O /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam -.. ok - -test_collate: - /build/reproducible-path/samtools-1.22.1/samtools collate -o /build/reproducible-path/samtools-1.22.1/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam -.. ok - -test_collate: - /build/reproducible-path/samtools-1.22.1/samtools collate -o /build/reproducible-path/samtools-1.22.1/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.22.1/test/collate/collate2.tmp -.. ok - -test_collate: - /build/reproducible-path/samtools-1.22.1/samtools collate --output-fmt=sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.22.1/test/collate/collate3.tmp -.. ok - -test_collate: - /build/reproducible-path/samtools-1.22.1/samtools collate --output-fmt=sam -f /build/reproducible-path/samtools-1.22.1/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.22.1/test/collate/1_fast_collate.sam -.. ok - -test_collate: - /build/reproducible-path/samtools-1.22.1/samtools collate --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.22.1/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.22.1/test/collate/2_fast_collate_with_tmp.sam -.. ok - -test_collate: - /build/reproducible-path/samtools-1.22.1/samtools collate -@ 2 --output-fmt=sam -O /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam -.. ok - -test_collate: - /build/reproducible-path/samtools-1.22.1/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.22.1/test/collate/collate1.tmp.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam -.. ok - -test_collate: - /build/reproducible-path/samtools-1.22.1/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.22.1/test/collate/collate2.tmp.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.22.1/test/collate/collate2.tmp -.. ok - -test_collate: - /build/reproducible-path/samtools-1.22.1/samtools collate -@ 2 --output-fmt=sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.22.1/test/collate/collate3.tmp -.. ok - -test_collate: - /build/reproducible-path/samtools-1.22.1/samtools collate -@ 2 --output-fmt=sam -f /build/reproducible-path/samtools-1.22.1/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.22.1/test/collate/1_fast_collate.sam -.. ok - -test_collate: - /build/reproducible-path/samtools-1.22.1/samtools collate -@ 2 --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.22.1/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.22.1/test/collate/2_fast_collate_with_tmp.sam -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/1_coord_sort.sam - - - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. - -.. expected failure - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/2_isize_overflow.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/3_reverse_read_pp_lt.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/4_reverse_read_pp_equal.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -cO sam /build/reproducible-path/samtools-1.22.1/test/fixmate/5_ct.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -cO sam /build/reproducible-path/samtools-1.22.1/test/fixmate/6_ct_replace.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/7_two_read_mapped.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/8_isize_overflow_64bit.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/sanitize.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ok+.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ok-.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_draft.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_not_updated.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_not_updated_noML.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_not_updated_noMN.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_bad_MN.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_MN_only.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ML_only.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ML_wrong_len.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_noseq.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_bounds.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/1_coord_sort.sam - - - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. - -.. expected failure - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/2_isize_overflow.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/3_reverse_read_pp_lt.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/4_reverse_read_pp_equal.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.22.1/test/fixmate/5_ct.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.22.1/test/fixmate/6_ct_replace.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/7_two_read_mapped.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/8_isize_overflow_64bit.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/sanitize.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ok+.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ok-.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_draft.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_not_updated.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_not_updated_noML.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_not_updated_noMN.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_bad_MN.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_MN_only.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ML_only.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_ML_wrong_len.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_noseq.sam - -.. ok - -test_fixmate: - /build/reproducible-path/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.22.1/test/fixmate/mod_bounds.sam - -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools calmd -uAr /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.ref.fa -.. ok - -/build/reproducible-path/samtools-1.22.1/samtools calmd -@ 2 -uAr /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.ref.fa -.. ok - -test_idxstat: - /build/reproducible-path/samtools-1.22.1/samtools idxstats /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -.. ok - -test_idxstat: - /build/reproducible-path/samtools-1.22.1/samtools idxstats /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.cram -.. ok - -test_idxstat: - /build/reproducible-path/samtools-1.22.1/samtools idxstats /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.sam -.. ok - -test_quickcheck: - /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/1.quickcheck.badeof.bam -.. ok - -test_quickcheck: - /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/2.quickcheck.badheader.bam -.. ok - -test_quickcheck: - /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/3.quickcheck.ok.bam -.. ok - -test_quickcheck: - /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/4.quickcheck.ok.bam -.. ok - -test_quickcheck: - /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram -.. ok - -test_quickcheck: - /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/6.quickcheck.cram21.ok.cram -.. ok - -test_quickcheck: - /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/7.quickcheck.cram30.ok.cram -.. ok - -test_quickcheck: - /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/8.quickcheck.cram21.truncated.cram -.. ok - -test_quickcheck: - /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/9.quickcheck.cram30.truncated.cram -.. ok - -test_quickcheck: - /build/reproducible-path/samtools-1.22.1/samtools quickcheck /build/reproducible-path/samtools-1.22.1/test/quickcheck/10.quickcheck.notargets.bam -.. ok - -test_quickcheck: - /build/reproducible-path/samtools-1.22.1/samtools quickcheck -v /build/reproducible-path/samtools-1.22.1/test/quickcheck/1.quickcheck.badeof.bam /build/reproducible-path/samtools-1.22.1/test/quickcheck/2.quickcheck.badheader.bam /build/reproducible-path/samtools-1.22.1/test/quickcheck/3.quickcheck.ok.bam /build/reproducible-path/samtools-1.22.1/test/quickcheck/4.quickcheck.ok.bam /build/reproducible-path/samtools-1.22.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram /build/reproducible-path/samtools-1.22.1/test/quickcheck/6.quickcheck.cram21.ok.cram /build/reproducible-path/samtools-1.22.1/test/quickcheck/7.quickcheck.cram30.ok.cram /build/reproducible-path/samtools-1.22.1/test/quickcheck/8.quickcheck.cram21.truncated.cram /build/reproducible-path/samtools-1.22.1/test/quickcheck/9.quickcheck.cram30.truncated.cram /build/reproducible-path/samtools-1.22.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' -.. ok - -test_quickcheck: - /build/reproducible-path/samtools-1.22.1/samtools quickcheck -uv /build/reproducible-path/samtools-1.22.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' -.. ok - -test_reheader: - /build/reproducible-path/samtools-1.22.1/samtools reheader /build/reproducible-path/samtools-1.22.1/test/reheader/hdr.sam /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' -.. ok - -test_reheader: - /build/reproducible-path/samtools-1.22.1/samtools reheader /build/reproducible-path/samtools-1.22.1/test/reheader/hdr.sam /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v21.cram | /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' -.. ok - -test_reheader: - /build/reproducible-path/samtools-1.22.1/samtools reheader /build/reproducible-path/samtools-1.22.1/test/reheader/hdr.sam /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' -.. ok - -test_reheader: - /build/reproducible-path/samtools-1.22.1/samtools reheader --in-place /build/reproducible-path/samtools-1.22.1/test/reheader/hdr.sam /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v21.cram && /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' -.. ok - -test_reheader: - /build/reproducible-path/samtools-1.22.1/samtools reheader --in-place /build/reproducible-path/samtools-1.22.1/test/reheader/hdr.sam /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v30.cram && /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' -.. ok - -test_reheader: - /build/reproducible-path/samtools-1.22.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' -.. ok - -test_reheader: - /build/reproducible-path/samtools-1.22.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.22.1/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -m overwrite_all /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -m orphan_only /build/reproducible-path/samtools-1.22.1/test/addrprg/2_fixup_orphan.sam -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -R '1#9' /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.22.1/test/addrprg/4_fixup_norg.sam -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.22.1/test/addrprg/4_fixup_norg.sam -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -m orphan_only /build/reproducible-path/samtools-1.22.1/test/addrprg/2_fixup_orphan.sam -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -R '1#9' /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.22.1/test/addrprg/4_fixup_norg.sam -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.22.1/test/addrprg/4_fixup_norg.sam -.. ok - -test_addrprg: - /build/reproducible-path/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.22.1/test/addrprg/1_fixup.sam -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/1_name_sort.sam - - - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. - - -.. expected failure - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/2_bad_order.sam - - - ERR: samtools markdup: error, not in coordinate sorted order. - - -.. expected failure - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/3_missing_mc.sam - - - ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. - -samtools markdup: error, unable to assign pair hash key. - - -.. expected failure - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/4_missing_ms.sam - - - ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. - -samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. - - -.. expected failure - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/5_markdup.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -O sam -r --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/6_remove_dups.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -S -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/7_mark_supp_dup.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/8_optical_dup.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/9_optical_dup_qcfail.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.22.1/test/markdup/10_optical_chain.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.22.1/test/markdup/10_optical_chain.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/11_optical_dup_regex.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/11_optical_dup_regex.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/12_optical_chain_regex.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/13_optical_barcode_tag.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/14_optical_barcode_name.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/15_optical_barcode_rgx_name.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/16_optical_barcode_rgx_name_test_2.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/17_read_group.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.22.1/test/markdup/18_primary_duplicate_count.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/1_name_sort.sam - - - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. - - -.. expected failure - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/2_bad_order.sam - - - ERR: samtools markdup: error, not in coordinate sorted order. - - -.. expected failure - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/3_missing_mc.sam - - - ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. - -samtools markdup: error, unable to assign pair hash key. - - -.. expected failure - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/4_missing_ms.sam - - - ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. - -samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. - - -.. expected failure - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/5_markdup.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -O sam -r --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/6_remove_dups.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/7_mark_supp_dup.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/8_optical_dup.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/9_optical_dup_qcfail.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.22.1/test/markdup/10_optical_chain.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.22.1/test/markdup/10_optical_chain.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/11_optical_dup_regex.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/11_optical_dup_regex.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/12_optical_chain_regex.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/13_optical_barcode_tag.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/14_optical_barcode_name.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/15_optical_barcode_rgx_name.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/16_optical_barcode_rgx_name_test_2.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.22.1/test/markdup/17_read_group.sam - -.. ok - -test_markdup: - /build/reproducible-path/samtools-1.22.1/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.22.1/test/markdup/18_primary_duplicate_count.sam - -.. ok - -test_bedcov: - /build/reproducible-path/samtools-1.22.1/samtools bedcov /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov.bam -.. ok - -test_bedcov: - /build/reproducible-path/samtools-1.22.1/samtools bedcov -j /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov.bam -.. ok - -test_bedcov: - /build/reproducible-path/samtools-1.22.1/samtools bedcov -g512 -G2048 /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov.bam -.. ok - -test_bedcov: - /build/reproducible-path/samtools-1.22.1/samtools bedcov -c /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.22.1/test/bedcov/bedcov.bam -.. ok - -.. ok - -.. ok - -.. ok - -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -d an -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.unk.sam /build/reproducible-path/samtools-1.22.1/test/split/split_d_nn.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split --output-fmt sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.0unk.sam /build/reproducible-path/samtools-1.22.1/test/split/split_d_nn.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -d an -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.22.1/test/split/split.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.unk.sam /build/reproducible-path/samtools-1.22.1/test/split/split_d_nn.sam -.. ok - -test_split: - /build/reproducible-path/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.22.1/test/split/split.tmp.d_nn.0unk.sam /build/reproducible-path/samtools-1.22.1/test/split/split_d_nn.sam -.. ok - -test_large_positions: - /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG /tmp/EQ6JAxW1Jo/longref.sam.gz -.. ok - -test_large_positions: - /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG /tmp/EQ6JAxW1Jo/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 -.. ok - -test_large_positions: - /build/reproducible-path/samtools-1.22.1/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.22.1/test/large_pos/test.bed /tmp/EQ6JAxW1Jo/longref.sam.gz -.. ok - -test_large_positions: - /build/reproducible-path/samtools-1.22.1/samtools sort -O sam --no-PG -m 10M /build/reproducible-path/samtools-1.22.1/test/large_pos/longref_name.sam -.. ok - -test_large_positions: - /build/reproducible-path/samtools-1.22.1/samtools merge -O sam --no-PG - /build/reproducible-path/samtools-1.22.1/test/large_pos/longref.sam /build/reproducible-path/samtools-1.22.1/test/large_pos/longref2.sam -.. ok - -test_large_positions: - /build/reproducible-path/samtools-1.22.1/samtools depth /build/reproducible-path/samtools-1.22.1/test/large_pos/longref.sam -.. ok - -test_large_positions: - /build/reproducible-path/samtools-1.22.1/samtools depth -b /build/reproducible-path/samtools-1.22.1/test/large_pos/test.bed /build/reproducible-path/samtools-1.22.1/test/large_pos/longref.sam -.. ok - -test_large_positions: - /build/reproducible-path/samtools-1.22.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/EQ6JAxW1Jo/longref.sam.gz -.. ok - -test_large_positions: - /build/reproducible-path/samtools-1.22.1/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | - /build/reproducible-path/samtools-1.22.1/samtools fixmate -O sam --no-PG - - | - /build/reproducible-path/samtools-1.22.1/samtools sort -O sam --no-PG -m 10M -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --primer-counts /build/reproducible-path/samtools-1.22.1/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/reproducible-path/samtools-1.22.1/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/2_both_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /build/reproducible-path/samtools-1.22.1/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/3_multi_ref_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/4_total_hc_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /build/reproducible-path/samtools-1.22.1/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/reproducible-path/samtools-1.22.1/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/2_both_test_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /build/reproducible-path/samtools-1.22.1/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/3_multi_ref_data.sam -.. ok - -test_ampliconclip: - /build/reproducible-path/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/4_total_hc_data.sam -.. ok - -test_ampliconstats: - /build/reproducible-path/samtools-1.22.1/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_hard_clipped.expected.sam /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_soft_clipped.expected.sam /build/reproducible-path/samtools-1.22.1/test/ampliconclip/1_soft_clipped_strand.expected.sam /build/reproducible-path/samtools-1.22.1/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' -.. ok - -test_ampliconstats: - /build/reproducible-path/samtools-1.22.1/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.22.1/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.22.1/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' -.. ok - -test_ampliconstats: - /build/reproducible-path/samtools-1.22.1/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.22.1/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' -.. ok - -test_reset: - cat /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag | /build/reproducible-path/samtools-1.22.1/samtools view -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag < /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.22.1/samtools view -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.22.1/samtools view -.. ok - -test_reset: - cat /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag -o /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag -o /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.bam -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag -o /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.22.1/test/dat/test_input_1_a.cram -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG sam_to_fixed_bam /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index --no-PG /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.22.1/test/reset/output.tmp.sam -e"@PG" -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG -o /build/reproducible-path/samtools-1.22.1/test/reset/output -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /build/reproducible-path/samtools-1.22.1/test/reset/output -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /build/reproducible-path/samtools-1.22.1/test/reset/output -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /build/reproducible-path/samtools-1.22.1/test/reset/output -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /build/reproducible-path/samtools-1.22.1/test/reset/output -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /build/reproducible-path/samtools-1.22.1/test/reset/output -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /build/reproducible-path/samtools-1.22.1/test/reset/output -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset --dupflag /build/reproducible-path/samtools-1.22.1/test/reset/seq.sam -o /build/reproducible-path/samtools-1.22.1/test/reset/output -.. ok - -test_reset: - /build/reproducible-path/samtools-1.22.1/samtools reset /build/reproducible-path/samtools-1.22.1/test/reset/seq.sam -o /build/reproducible-path/samtools-1.22.1/test/reset/output -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum /build/reproducible-path/samtools-1.22.1/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum -a /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum -qv /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum -qv -a /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum -m /build/reproducible-path/samtools-1.22.1/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum -m /build/reproducible-path/samtools-1.22.1/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 /build/reproducible-path/samtools-1.22.1/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 -a /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 -qv /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 -qv -a /build/reproducible-path/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 -m /build/reproducible-path/samtools-1.22.1/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - -test_checksum: - /build/reproducible-path/samtools-1.22.1/samtools checksum -@ 2 -m /build/reproducible-path/samtools-1.22.1/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' -.. ok - - -Number of tests: - total .. 1009 - passed .. 964 - failed .. 0 - expected failure .. 45 - unexpected pass .. 0 - -test/merge/test_bam_translate test/merge/test_bam_translate.tmp -test/merge/test_rtrans_build -test/merge/test_trans_tbl_init -cd test/mpileup && AWK="mawk" ../regression.sh mpileup.reg - -=== Testing mpileup.reg regressions === -[W::cram_encode_aux] Missing @RG header for RG "ERR162872" -[W::cram_encode_aux] Missing @RG header for RG "ERR162872" -[W::cram_encode_aux] Missing @RG header for RG "ERR162872" -[W::cram_encode_aux] Missing @RG header for RG "ERR162872" - -EXPECTED FAIL: Task failed, but expected to fail; -when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam - -Expected passes: 120 -Unexpected passes: 0 -Expected failures: 1 -Unexpected failures: 0 -=> PASS -cd test/mpileup && AWK="mawk" ../regression.sh depth.reg - -=== Testing depth.reg regressions === - -EXPECTED FAIL: Task failed, but expected to fail; -when running $samtools depth -a -b xx.bed3 xx#depth3.bam - -Expected passes: 55 -Unexpected passes: 0 -Expected failures: 1 -Unexpected failures: 0 -=> PASS -cd test/mpileup && AWK="mawk" ../regression.sh cram-size.reg - -=== Testing cram-size.reg regressions === - -Expected passes: 5 -Unexpected passes: 0 -Expected failures: 0 -Unexpected failures: 0 -=> PASS -cd test/consensus && AWK="mawk" ../regression.sh consensus.reg - -=== Testing consensus.reg regressions === - -Expected passes: 77 -Unexpected passes: 0 -Expected failures: 0 -Unexpected failures: 0 -=> PASS -cd test/consensus && AWK="mawk" PARAM="-@4 -Z4" ../regression.sh consensus.reg - -=== Testing consensus.reg regressions === - -Expected passes: 77 -Unexpected passes: 0 -Expected failures: 0 -Unexpected failures: 0 -=> PASS -cd test/cram_size && AWK="mawk" ../regression.sh cram_size.reg - -=== Testing cram_size.reg regressions === - -Expected passes: 3 -Unexpected passes: 0 -Expected failures: 0 -Unexpected failures: 0 -=> PASS -make[2]: Leaving directory '/build/reproducible-path/samtools-1.22.1' - rm -fr -- /tmp/dh-xdg-rundir-sUWOZ6sn -make[1]: Leaving directory '/build/reproducible-path/samtools-1.22.1' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/samtools.substvars debian/samtools-test.substvars @@ -4212,7 +953,7 @@ dh_auto_install -- \ prefix=/usr install -m0755 -d /build/reproducible-path/samtools-1.22.1/debian/tmp - make -j12 install DESTDIR=/build/reproducible-path/samtools-1.22.1/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr + make -j16 install DESTDIR=/build/reproducible-path/samtools-1.22.1/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/reproducible-path/samtools-1.22.1' mkdir -p -m 755 /build/reproducible-path/samtools-1.22.1/debian/tmp/usr/bin /build/reproducible-path/samtools-1.22.1/debian/tmp/usr/bin /build/reproducible-path/samtools-1.22.1/debian/tmp/usr/share/man/man1 install -p samtools /build/reproducible-path/samtools-1.22.1/debian/tmp/usr/bin @@ -4271,12 +1012,12 @@ debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/samtools-1.22.1' dh_installchangelogs NEWS.md - install -m0755 -d debian/samtools/usr/share/doc/samtools - install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed debian/samtools/usr/share/doc/samtools/changelog.Debian - install -p -m0644 NEWS.md debian/samtools/usr/share/doc/samtools/changelog install -m0755 -d debian/samtools-test/usr/share/doc/samtools-test install -p -m0644 debian/.debhelper/generated/samtools-test/dh_installchangelogs.dch.trimmed debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian install -p -m0644 NEWS.md debian/samtools-test/usr/share/doc/samtools-test/changelog + install -m0755 -d debian/samtools/usr/share/doc/samtools + install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed debian/samtools/usr/share/doc/samtools/changelog.Debian + install -p -m0644 NEWS.md debian/samtools/usr/share/doc/samtools/changelog make[1]: Leaving directory '/build/reproducible-path/samtools-1.22.1' dh_installexamples install -m0755 -d debian/samtools/usr/share/doc/samtools/examples @@ -4298,72 +1039,80 @@ dh_installman rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-checksum.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 - mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-checksum.1 debian/samtools/usr/share/man/man1/samtools-collate.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 - mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 - mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 + mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 + mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 + mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 + mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 + mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 + mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 mv debian/samtools/usr/share/man/man1/samtools-checksum.1.dh-new debian/samtools/usr/share/man/man1/samtools-checksum.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-checksum.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 - mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 - mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 - mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 - mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 - mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 - mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 - mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 - mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 - mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-checksum.1 debian/samtools/usr/share/man/man1/samtools-collate.1 + mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 + mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 + mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 + mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 + mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 + mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 + mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 + mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 + mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 + mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 + mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 + mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 - mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 - mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 - mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 - mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 - mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 - mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 - mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 - mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 + mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 + mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 + mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 + mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 + mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 + mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 - mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 - mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 - mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 - mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 + mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 - mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 - chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 + chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 dh_lintian install -m0755 -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools @@ -4412,26 +1161,21 @@ objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug dh_strip -a - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80/6442eca6fd2106fa94499dae6b16a168381ca1.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80/6442eca6fd2106fa94499dae6b16a168381ca1.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80/6442eca6fd2106fa94499dae6b16a168381ca1.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fc objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fc/d9a9eeaa25b4e832d46b028fb1d07eb69584f7.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fc/d9a9eeaa25b4e832d46b028fb1d07eb69584f7.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fc/d9a9eeaa25b4e832d46b028fb1d07eb69584f7.debug debian/samtools/usr/bin/maq2sam-short - install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6 - objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/5f52e916d5c087fb56d4273c998c4d7c875db4.debug - chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/5f52e916d5c087fb56d4273c998c4d7c875db4.debug - strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa - objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/5f52e916d5c087fb56d4273c998c4d7c875db4.debug debian/samtools/usr/bin/md5fa install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad/7d003fbfb50d76237edba057f5b84b1c3ab792.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad/7d003fbfb50d76237edba057f5b84b1c3ab792.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad/7d003fbfb50d76237edba057f5b84b1c3ab792.debug debian/samtools/usr/bin/samtools + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80/6442eca6fd2106fa94499dae6b16a168381ca1.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80/6442eca6fd2106fa94499dae6b16a168381ca1.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80/6442eca6fd2106fa94499dae6b16a168381ca1.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/90 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/90/6e24a8bc98a15882dadb58130fca9cd405732c.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/90/6e24a8bc98a15882dadb58130fca9cd405732c.debug @@ -4442,6 +1186,11 @@ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/c96d2a19ee2f7e1c93b26d8e28ce6abe7a1ab8.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/c96d2a19ee2f7e1c93b26d8e28ce6abe7a1ab8.debug debian/samtools/usr/bin/ace2sam + install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6 + objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/5f52e916d5c087fb56d4273c998c4d7c875db4.debug + chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/5f52e916d5c087fb56d4273c998c4d7c875db4.debug + strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa + objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/5f52e916d5c087fb56d4273c998c4d7c875db4.debug debian/samtools/usr/bin/md5fa install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e6 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e6/fafeac55041e882097a31b852ed95527c763ab.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e6/fafeac55041e882097a31b852ed95527c763ab.debug @@ -4458,20 +1207,20 @@ rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN - dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite + dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite dh_installdeb install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN dh_gencontrol - install -m0755 -d debian/samtools-test/DEBIAN - echo misc:Depends= >> debian/samtools-test.substvars - echo misc:Pre-Depends= >> debian/samtools-test.substvars - dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test install -m0755 -d debian/samtools/DEBIAN echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=samtools-dbgsym -DDepends="samtools (= \${binary:Version})" -DDescription="debug symbols for samtools" -DBuild-Ids="806442eca6fd2106fa94499dae6b16a168381ca1 906e24a8bc98a15882dadb58130fca9cd405732c ad7d003fbfb50d76237edba057f5b84b1c3ab792 c65f52e916d5c087fb56d4273c998c4d7c875db4 cdc96d2a19ee2f7e1c93b26d8e28ce6abe7a1ab8 e6fafeac55041e882097a31b852ed95527c763ab fcd9a9eeaa25b4e832d46b028fb1d07eb69584f7" -DSection=debug -UMulti-Arch -UReplaces -UBreaks + install -m0755 -d debian/samtools-test/DEBIAN + echo misc:Depends= >> debian/samtools-test.substvars + echo misc:Pre-Depends= >> debian/samtools-test.substvars + dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/samtools @@ -4493,9 +1242,9 @@ dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb --root-owner-group --build debian/samtools-test .. -dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.22.1-1_amd64.deb'. -dpkg-deb: building package 'samtools' in '../samtools_1.22.1-1_amd64.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.22.1-1_all.deb'. +dpkg-deb: building package 'samtools' in '../samtools_1.22.1-1_amd64.deb'. +dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.22.1-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../samtools_1.22.1-1_amd64.buildinfo dpkg-genchanges --build=binary -O../samtools_1.22.1-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4504,12 +1253,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/81351/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/81351/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/939202 and its subdirectories -I: Current time: Tue Nov 11 05:55:41 -12 2025 -I: pbuilder-time-stamp: 1762883741 +I: removing directory /srv/workspace/pbuilder/81351 and its subdirectories +I: Current time: Tue Dec 15 14:20:32 +14 2026 +I: pbuilder-time-stamp: 1797294032