I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 21 15:42:25 +14 2024 I: pbuilder-time-stamp: 1732153345 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [htslib_1.21+ds-0+exp2.dsc] I: copying [./htslib_1.21+ds.orig.tar.bz2] I: copying [./htslib_1.21+ds-0+exp2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Nov 13 20:18:27 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./htslib_1.21+ds-0+exp2.dsc: no acceptable signature found dpkg-source: info: extracting htslib in htslib-1.21+ds dpkg-source: info: unpacking htslib_1.21+ds.orig.tar.bz2 dpkg-source: info: unpacking htslib_1.21+ds-0+exp2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_git_version dpkg-source: info: applying define_PATH_MAX.patch dpkg-source: info: applying fPIC.patch dpkg-source: info: applying testShebang.patch dpkg-source: info: applying fix_float_precision dpkg-source: info: applying fix_sequence_of_linked_libs.patch dpkg-source: info: applying trim-file-prefix.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/14935/tmp/hooks/D01_modify_environment starting debug: Running on virt64z. 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 Nov 21 01:42 /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/14935/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/14935/tmp/hooks/D02_print_environment starting I: set 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]="2" [2]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=experimental EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=19110b64d7dd444eab67038223058073 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=14935 PS4='+ ' 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.yWXLEUA6/pbuilderrc_KluO --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.yWXLEUA6/b2 --logfile b2/build.log htslib_1.21+ds-0+exp2.dsc' SUDO_GID=110 SUDO_UID=103 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-27-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/14935/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19686 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev; however: Package libcurl4-gnutls-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libdeflate-dev; however: Package libdeflate-dev is not installed. pbuilder-satisfydepends-dummy depends on libhtscodecs-dev (>= 1.0); however: Package libhtscodecs-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhtscodecs-dev{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 87 newly installed, 0 to remove and 0 not upgraded. Need to get 36.0 MB of archives. After unpacking 112 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-11 [83.6 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.1-1+b1 [22.3 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf comerr-dev armhf 2.1-1.47.1-1+b1 [54.3 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 24 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 35 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf libgssrpc4t64 armhf 1.21.3-3 [52.5 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf libkadm5clnt-mit12 armhf 1.21.3-3 [37.0 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf libkdb5-10t64 armhf 1.21.3-3 [37.1 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf libkadm5srv-mit12 armhf 1.21.3-3 [46.7 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf krb5-multidev armhf 1.21.3-3 [126 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf libbrotli-dev armhf 1.1.0-2+b6 [293 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf libbz2-dev armhf 1.0.8-6 [28.7 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3+b1 [163 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf libnghttp3-9 armhf 1.4.0-1+b1 [55.0 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf libngtcp2-16 armhf 1.6.0-1 [118 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls8 armhf 1.6.0-1 [17.1 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf libcurl3t64-gnutls armhf 8.11.0-1 [310 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10+b1 [164 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf libunbound8 armhf 1.22.0-1 [539 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf libgnutls-dane0t64 armhf 3.8.8-2 [440 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf libgnutls-openssl27t64 armhf 3.8.8-2 [440 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf libidn2-dev armhf 2.3.7-2+b1 [119 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf libp11-kit-dev armhf 0.25.5-2+b1 [208 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf libtasn1-6-dev armhf 4.19.0-3+b3 [93.2 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-2+b2 [328 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf libgmp-dev armhf 2:6.3.0+dfsg-2+b2 [593 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf nettle-dev armhf 3.10-1+b1 [1313 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf libgnutls28-dev armhf 3.8.8-2 [1328 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libkrb5-dev armhf 1.21.3-3 [15.8 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf libldap-dev armhf 2.5.18+dfsg-3+b1 [282 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB] Get: 71 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB] Get: 72 http://deb.debian.org/debian unstable/main armhf libnghttp2-dev armhf 1.64.0-1 [103 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf libnghttp3-dev armhf 1.4.0-1+b1 [79.8 kB] Get: 74 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls-dev armhf 1.6.0-1 [22.1 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf libngtcp2-dev armhf 1.6.0-1 [168 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf libpsl-dev armhf 0.21.2-1.1+b1 [76.8 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2+b5 [63.6 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf libssl-dev armhf 3.3.2-2 [2385 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf libssh2-1-dev armhf 1.11.1-1 [378 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf libzstd-dev armhf 1.5.6+dfsg-1+b1 [327 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf libcurl4-gnutls-dev armhf 8.11.0-1 [434 kB] Get: 83 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.22-1 [36.3 kB] Get: 84 http://deb.debian.org/debian unstable/main armhf libdeflate-dev armhf 1.22-1 [44.5 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf libhtscodecs2 armhf 1.6.1-1 [63.1 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf libhtscodecs-dev armhf 1.6.1-1 [2964 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf liblzma-dev armhf 5.6.3-1+b1 [304 kB] Fetched 36.0 MB in 1s (62.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19686 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_armhf.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_armhf.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_armhf.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../15-libcom-err2_1.47.1-1+b1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.1-1+b1) ... Selecting previously unselected package comerr-dev:armhf. Preparing to unpack .../16-comerr-dev_2.1-1.47.1-1+b1_armhf.deb ... Unpacking comerr-dev:armhf (2.1-1.47.1-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... 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Setting up libkeyutils1:armhf (1.6.3-4) ... Setting up libicu72:armhf (72.1-5+b1) ... Setting up libzstd-dev:armhf (1.5.6+dfsg-1+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:armhf (1.1.0-2+b6) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up libpsl5t64:armhf (0.21.2-1.1+b1) ... Setting up libnghttp2-14:armhf (1.64.0-1) ... Setting up libdeflate0:armhf (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ... Setting up libcom-err2:armhf (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up libpsl-dev:armhf (0.21.2-1.1+b1) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Setting up libhtscodecs-dev:armhf (1.6.1-1) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:armhf (1.22.0-1) ... Setting up libpkgconf3:armhf (1.8.1-4) ... Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2+b2) ... Setting up libgnutls-dane0t64:armhf (3.8.8-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up comerr-dev:armhf (2.1-1.47.1-1+b1) ... Setting up libssl-dev:armhf (3.3.2-2) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up libidn2-dev:armhf (2.3.7-2+b1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:armhf (1.4.0-1+b1) ... Setting up libnghttp3-dev:armhf (1.4.0-1+b1) ... Setting up liblzma-dev:armhf (5.6.3-1+b1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libngtcp2-16:armhf (1.6.0-1) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libssh2-1t64:armhf (1.11.1-1) ... Setting up libtasn1-6-dev:armhf (4.19.0-3+b3) ... Setting up libdeflate-dev:armhf (1.22-1) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbrotli-dev:armhf (1.1.0-2+b6) ... Setting up libngtcp2-crypto-gnutls8:armhf (1.6.0-1) ... Setting up libp11-kit-dev:armhf (0.25.5-2+b1) ... Setting up libbz2-dev:armhf (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:armhf (2:6.3.0+dfsg-2+b2) ... Setting up nettle-dev:armhf (3.10-1+b1) ... Setting up libtool (2.4.7-8) ... Setting up libngtcp2-crypto-gnutls-dev:armhf (1.6.0-1) ... Setting up libngtcp2-dev:armhf (1.6.0-1) ... Setting up libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Setting up pkgconf:armhf (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:armhf (2.5.18+dfsg-3+b1) ... Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libssh2-1-dev:armhf (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:armhf (3.8.8-2) ... Setting up libnghttp2-dev:armhf (1.64.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:armhf (8.11.0-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:armhf (1.21.3-3) ... Setting up librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5clnt-mit12:armhf (1.21.3-3) ... Setting up libkdb5-10t64:armhf (1.21.3-3) ... Setting up debhelper (13.20) ... Setting up libkadm5srv-mit12:armhf (1.21.3-3) ... Setting up krb5-multidev:armhf (1.21.3-3) ... Setting up libkrb5-dev:armhf (1.21.3-3) ... Setting up libcurl4-gnutls-dev:armhf (8.11.0-1) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/14935/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for experimental I: user script /srv/workspace/pbuilder/14935/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/htslib-1.21+ds/ && 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 > ../htslib_1.21+ds-0+exp2_source.changes dpkg-buildpackage: info: source package htslib dpkg-buildpackage: info: source version 1.21+ds-0+exp2 dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from htslib-1.21+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/htslib-1.21+ds' dh_auto_clean make -j4 distclean make[2]: Entering directory '/build/reproducible-path/htslib-1.21+ds' rm -f test/*.tmp test/*.tmp.* test/faidx/*.tmp* \ test/longrefs/*.tmp.* test/tabix/*.tmp.* \ test/bgzf_boundaries/*.tmp.* test/*/FAIL* \ header-exports.txt shlib-exports-so.txt rm -f libhts.so libhts.so.* rm -rf htscodecs/tests/test.out rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM config_vars.h version.h rm -f htscodecs/htscodecs/*.o htscodecs/htscodecs/*.pico rm -f hts-object-files rm -f htscodecs/tests/*.o rm -f libhts.a annot-tsv bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/pileup_mod test/plugins-dlhts test/sam test/test_bgzf test/test_expr test/test_faidx test/test_kfunc test/test_khash test/test_kstring test/test_mod test/test_nibbles test/test_realn test/test-regidx test/test_str2int test/test_time_funcs test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/test_introspection test/test-bcf_set_variant_type test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7 rm -f htscodecs/tests/rans4x8 htscodecs/tests/rans4x16pr htscodecs/tests/arith_dynamic htscodecs/tests/tokenise_name3 htscodecs/tests/fqzcomp_qual htscodecs/tests/varint rm -f config.cache config.h config.log config.mk config.status rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk htscodecs.mk rm -rf autom4te.cache make[2]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' rm -rf test_backup/ make[1]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/libhts3t64.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files rm -fr -- debian/libhts3t64/ debian/tmp/ debian/libhts-dev/ debian/htslib-test/ debian/tabix/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config cp -an --reflink=auto config.guess debian/.debhelper/bucket/files/ec2577614252326f889df1de97b9a457c03a9a94811048563c211a44496d8ba3.tmp mv debian/.debhelper/bucket/files/ec2577614252326f889df1de97b9a457c03a9a94811048563c211a44496d8ba3.tmp debian/.debhelper/bucket/files/ec2577614252326f889df1de97b9a457c03a9a94811048563c211a44496d8ba3 cp -f /usr/share/misc/config.guess ./config.guess cp -an --reflink=auto config.sub debian/.debhelper/bucket/files/465c5fe67c7d36b72e808812716445d4d38d4b94734ca8d36a8639d12323878b.tmp mv debian/.debhelper/bucket/files/465c5fe67c7d36b72e808812716445d4d38d4b94734ca8d36a8639d12323878b.tmp debian/.debhelper/bucket/files/465c5fe67c7d36b72e808812716445d4d38d4b94734ca8d36a8639d12323878b cp -f /usr/share/misc/config.sub ./config.sub dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/htslib-1.21+ds' # create clean copy of test dir cp -a test test_backup # to help with cross building, otherwise MMAP might get turned off export ac_cv_func_mmap_fixed_mapped=yes \ && autoconf \ && dh_auto_configure -- \ --enable-libcurl \ --enable-gcs \ --enable-s3 \ --enable-plugins \ --with-plugin-dir='/usr/lib/arm-linux-gnueabihf/htslib' \ --with-external-htscodecs \ --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/arm-linux-gnueabihf/htslib' ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir=/usr/lib/arm-linux-gnueabihf/htslib --with-external-htscodecs --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/arm-linux-gnueabihf/htslib checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... no checking whether __cpuid_count is declared... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc option to enable large file support... none needed checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for getpagesize... yes checking for working mmap... (cached) yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes checking for library containing dlsym... none required checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for htscodecs/rANS_static4x16.h... yes checking for rans_compress_bound_4x16 in -lhtscodecs... yes checking for libdeflate.h... yes checking for libdeflate_deflate_compress in -ldeflate... yes checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_external.mk to htscodecs.mk make[1]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/htslib-1.21+ds' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.21" \ libdir=/usr/lib/arm-linux-gnueabihf make -j4 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.21 libdir=/usr/lib/arm-linux-gnueabihf make[2]: Entering directory '/build/reproducible-path/htslib-1.21+ds' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.21"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'gcc' \ '-I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2' \ '-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects' \ '-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic' \ '-ldeflate -lhtscodecs -llzma -lbz2 -lz -lm ' \ | sed 's/-ffile-prefix-map=[^ ]*=.//' \ > config_vars.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_mods.o sam_mods.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o simd.o simd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/arm-linux-gnueabihf/htslib\" -c -o plugin.o plugin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_expr.pico hts_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam_mods.pico sam_mods.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o simd.pico simd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/arm-linux-gnueabihf/htslib\" -fPIC -c -o plugin.pico plugin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o annot-tsv.o annot-tsv.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup_mod.o test/pileup_mod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_expr.o test/test_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_faidx.o test/test_faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kfunc.o test/test_kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_khash.o test/test_khash.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kstring.o test/test_kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_mod.o test/test_mod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_nibbles.o test/test_nibbles.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_str2int.o test/test_str2int.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_time_funcs.o test/test_time_funcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_index.o test/test_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_introspection.o test/test_introspection.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico simd.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico plugin.pico -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm ln -sf libhts.so libhts.so.3 gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o simd.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o plugin.o ranlib libhts.a gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_khash test/test_khash.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_nibbles test/test_nibbles.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread make[2]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' make[1]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/htslib-1.21+ds' dh_auto_test -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.21" \ libdir=/usr/lib/arm-linux-gnueabihf \ || \ if find . -name "FAIL*" > /dev/null ; then \ for file in $(find . -name "FAIL*"); do echo ${file}; cat ${file}; done && false ; \ fi make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.21 libdir=/usr/lib/arm-linux-gnueabihf make[2]: Entering directory '/build/reproducible-path/htslib-1.21+ds' test/hts_endian test/test_expr test/test_kfunc test/test_khash test/test_kstring test/test_nibbles -v test/test_str2int test/test_time_funcs test/fieldarith test/fieldarith.sam test/hfile if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ fi if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ fi test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" Expected error: [E::hts_parse_region] Unexpected string "x" after region Expected error: [E::hts_parse_region] Unexpected string "y" after region Expected error: [E::hts_parse_region] Unexpected string "chr3" after region cd test/faidx && ./test-faidx.sh faidx.tst Testing faidx... PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_fetch FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t faidx_fetch_seq64 FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi CHROMOSOME_I:5001-5125 CHROMOSOME_X:101-225 Expected passes: 25 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/sam_filter && ./filter.sh filter.tst Testing sam_filter... PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@' Expected passes: 18 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tabix && ./test-tabix.sh tabix.tst Testing tabix... PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz -@ 2 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 --threads 2 Expected passes: 16 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/mpileup && ./test-pileup.sh mpileup.tst Testing (m)pileup... PASS : $pileup mp_D.sam PASS : $pileup -m mp_D.sam PASS : $pileup mp_DI.sam PASS : $pileup -m mp_DI.sam PASS : $pileup mp_I.sam PASS : $pileup -m mp_I.sam PASS : $pileup mp_P.sam PASS : $pileup -m mp_P.sam PASS : $pileup mp_ID.sam PASS : $pileup -m mp_ID.sam PASS : $pileup mp_N.sam PASS : $pileup -m mp_N.sam PASS : $pileup mp_N2.sam PASS : $pileup -m mp_N2.sam PASS : $pileup c1#pad1.sam PASS : $pileup -m c1#pad1.sam PASS : $pileup c1#pad2.sam PASS : $pileup -m c1#pad2.sam PASS : $pileup c1#pad3.sam PASS : $pileup -m c1#pad3.sam PASS : $pileup -m small.bam PASS : $pileup -m mp_overlap1.sam PASS : $pileup -m mp_overlap2.sam Expected passes: 23 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/fastq && ./test-fastq.sh Testing fastq support PASS : $tview minimal.fq PASS : $tview minimal.fa PASS : $tview multiline.fq PASS : $tview multiline.fa PASS : $tview -i fastq_aux longline.fq PASS : $tview single.fq PASS : $tview single.fa PASS : $tview -i fastq_aux single.fq PASS : $tview -i fastq_aux single.fa PASS : $tview interleaved.fq PASS : $tview interleaved.fa PASS : $tview -i fastq_aux interleaved.fq PASS : $tview -i fastq_aux interleaved.fa PASS : $tview -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_casava filter_casava.fq PASS : $tview -i fastq_casava filter_casava.fa PASS : $tview -i fastq_aux r1.fq PASS : $tview -i fastq_aux r2.fq PASS : $tview -i fastq_aux r1.fa PASS : $tview -i fastq_aux r2.fa PASS : $tview -i fastq_name2 name2.fq PASS : $tview -i fastq_name2 name2.fa PASS : $tview -f minimal.sam PASS : $tview -F minimal.sam PASS : $tview -f -o fastq_aux single_aux.sam PASS : $tview -F -o fastq_aux single_aux.sam PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -f -o fastq_casava inter_casava.sam PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -F -o fastq_casava inter_casava.sam PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -f -o fastq_casava filter_casava.sam PASS : $tview -F -o fastq_casava filter_casava.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam Expected passes: 41 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/base_mods && ./base-mods.sh base-mods.tst Testing base-modifications... PASS : $test_mod MM-chebi.sam PASS : $test_mod MM-double.sam PASS : $test_mod MM-multi.sam PASS : $test_mod MM-explicit.sam PASS : $test_mod -x MM-explicit.sam PASS : $test_mod -f 1 MM-explicit.sam PASS : $test_mod MM-not-all-modded.sam PASS : $pileup_mod < MM-pileup.sam PASS : $pileup_mod < MM-pileup2.sam PASS : $pileup_mod < MM-MNp.sam PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-MNf1.sam (must exit non-zero) PASS : $test_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-bounds+.sam (must exit non-zero) PASS : $test_mod < MM-bounds-.sam (must exit non-zero) Expected passes: 16 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq (Expect trailing 'x' message for " -1,001x") [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] (Expect trailing 'k' message for "1.5e+3k") [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] (Expect dropped fraction message for "12.3456k") [W::hts_parse_decimal] Discarding fractional part of 12.3456k [W::hts_parse_decimal] Discarding fractional part of 12.3456k (Expect invalid numeric message for "A") [W::hts_parse_decimal] Invalid numeric value A[truncated] (Expect invalid numeric message for "G") [W::hts_parse_decimal] Invalid numeric value G[truncated] (Expect invalid numeric message for " +/-") [W::hts_parse_decimal] Invalid numeric value +/-[truncated] (Expect invalid numeric message for " -.e+9999") [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] test/test-regidx cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} bgzip round-trip no threads: .. ok bgzip text mode round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip multifile no threads: .. ok bgzip --output no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip text mode round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok bgzip multifile 4 threads: .. ok bgzip --output 4 threads: .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -l 0 -b -m 14 -x /tmp/sXuEvDEUW2/index.bam.csi /build/reproducible-path/htslib-1.21+ds/test/index.sam > /tmp/sXuEvDEUW2/index.bam .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -c /tmp/sXuEvDEUW2/index.bam .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -l 0 -b -m 0 -x /tmp/sXuEvDEUW2/index.bam.bai /build/reproducible-path/htslib-1.21+ds/test/index.sam > /tmp/sXuEvDEUW2/index.bam .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -b /tmp/sXuEvDEUW2/index.bam .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -l 0 -z -m 14 -x /tmp/sXuEvDEUW2/index.sam.gz.csi /build/reproducible-path/htslib-1.21+ds/test/index.sam > /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -c /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -l 0 -z -m 0 -x /tmp/sXuEvDEUW2/index.sam.gz.bai /build/reproducible-path/htslib-1.21+ds/test/index.sam > /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -b /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -l 0 -z -m 14 -x /tmp/sXuEvDEUW2/index.sam.gz.csi /build/reproducible-path/htslib-1.21+ds/test/index_dos.sam > /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -c /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -l 0 -z -m 0 -x /tmp/sXuEvDEUW2/index.sam.gz.bai /build/reproducible-path/htslib-1.21+ds/test/index_dos.sam > /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -b /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -l 0 -C -x /tmp/sXuEvDEUW2/index.cram.crai /build/reproducible-path/htslib-1.21+ds/test/index.sam > /tmp/sXuEvDEUW2/index.cram .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index /tmp/sXuEvDEUW2/index.cram .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -l 0 -b -m 14 -x /tmp/sXuEvDEUW2/index.bcf.csi /build/reproducible-path/htslib-1.21+ds/test/index.vcf > /tmp/sXuEvDEUW2/index.bcf .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -c /tmp/sXuEvDEUW2/index.bcf .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -l 0 -z -m 14 -x /tmp/sXuEvDEUW2/index.vcf.gz.csi /build/reproducible-path/htslib-1.21+ds/test/index.vcf > /tmp/sXuEvDEUW2/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -c /tmp/sXuEvDEUW2/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -l 0 -z -m 0 -x /tmp/sXuEvDEUW2/index.vcf.gz.tbi /build/reproducible-path/htslib-1.21+ds/test/index.vcf > /tmp/sXuEvDEUW2/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -t /tmp/sXuEvDEUW2/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/tabix /tmp/sXuEvDEUW2/index.vcf.gz##idx##/tmp/sXuEvDEUW2/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view /tmp/sXuEvDEUW2/index2.bam 1:1000000-1000000 .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view /tmp/sXuEvDEUW2/index2.bam 1:2000000-2000000 .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view /tmp/sXuEvDEUW2/index2.bam 2:1000000-1000000 .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view /tmp/sXuEvDEUW2/index2.bam 2:2000000-2000000 .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/sXuEvDEUW2/index.bam.csi /build/reproducible-path/htslib-1.21+ds/test/index.sam > /tmp/sXuEvDEUW2/index.bam .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -c /tmp/sXuEvDEUW2/index.bam .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -@4 -l 0 -b -m 0 -x /tmp/sXuEvDEUW2/index.bam.bai /build/reproducible-path/htslib-1.21+ds/test/index.sam > /tmp/sXuEvDEUW2/index.bam .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -b /tmp/sXuEvDEUW2/index.bam .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/sXuEvDEUW2/index.sam.gz.csi /build/reproducible-path/htslib-1.21+ds/test/index.sam > /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -c /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/sXuEvDEUW2/index.sam.gz.bai /build/reproducible-path/htslib-1.21+ds/test/index.sam > /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -b /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/sXuEvDEUW2/index.sam.gz.csi /build/reproducible-path/htslib-1.21+ds/test/index_dos.sam > /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -c /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/sXuEvDEUW2/index.sam.gz.bai /build/reproducible-path/htslib-1.21+ds/test/index_dos.sam > /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -b /tmp/sXuEvDEUW2/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -@4 -l 0 -C -x /tmp/sXuEvDEUW2/index.cram.crai /build/reproducible-path/htslib-1.21+ds/test/index.sam > /tmp/sXuEvDEUW2/index.cram .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index /tmp/sXuEvDEUW2/index.cram .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/sXuEvDEUW2/index.bcf.csi /build/reproducible-path/htslib-1.21+ds/test/index.vcf > /tmp/sXuEvDEUW2/index.bcf .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -c /tmp/sXuEvDEUW2/index.bcf .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/sXuEvDEUW2/index.vcf.gz.csi /build/reproducible-path/htslib-1.21+ds/test/index.vcf > /tmp/sXuEvDEUW2/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -c /tmp/sXuEvDEUW2/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/sXuEvDEUW2/index.vcf.gz.tbi /build/reproducible-path/htslib-1.21+ds/test/index.vcf > /tmp/sXuEvDEUW2/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_index -t /tmp/sXuEvDEUW2/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.21+ds/tabix /tmp/sXuEvDEUW2/index.vcf.gz##idx##/tmp/sXuEvDEUW2/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view /tmp/sXuEvDEUW2/index2.bam 1:1000000-1000000 .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view /tmp/sXuEvDEUW2/index2.bam 1:2000000-2000000 .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view /tmp/sXuEvDEUW2/index2.bam 2:1000000-1000000 .. ok test_index: /build/reproducible-path/htslib-1.21+ds/test/test_view /tmp/sXuEvDEUW2/index2.bam 2:2000000-2000000 .. ok test_view testing multi-ref CRAM modes: ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing multi-ref CRAM modes: ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /build/reproducible-path/htslib-1.21+ds/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -@4 -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -@4 -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -@4 -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /build/reproducible-path/htslib-1.21+ds/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_MD testing xx#MD.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ Checking for MD/NM in xx#MD.sam ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_MD testing xx#MD2.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_vcf_api: /build/reproducible-path/htslib-1.21+ds/test/test-vcf-api /tmp/sXuEvDEUW2/test-vcf-api.bcf .. ok test_bcf2vcf: /build/reproducible-path/htslib-1.21+ds/test/test_view /build/reproducible-path/htslib-1.21+ds/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /build/reproducible-path/htslib-1.21+ds/test/test-vcf-sweep /tmp/sXuEvDEUW2/test-vcf-api.bcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.21+ds/htsfile -ch /build/reproducible-path/htslib-1.21+ds/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.21+ds/htsfile -c /build/reproducible-path/htslib-1.21+ds/test/formatcols.vcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.21+ds/htsfile -c /build/reproducible-path/htslib-1.21+ds/test/noroundtrip.vcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.21+ds/htsfile -c /build/reproducible-path/htslib-1.21+ds/test/formatmissing.vcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.21+ds/htsfile -c /build/reproducible-path/htslib-1.21+ds/test/vcf_meta_meta.vcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.21+ds/test/test_view /build/reproducible-path/htslib-1.21+ds/test/modhdr.vcf.gz chr22:1-2 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/sXuEvDEUW2 -s 74452500 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/sXuEvDEUW2 -s 34270147 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/sXuEvDEUW2 -s 11108528 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/sXuEvDEUW2 -s 42233895 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/sXuEvDEUW2 -s 8111117 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/sXuEvDEUW2 -s 85644070 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/sXuEvDEUW2 -s 49879942 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/sXuEvDEUW2 -s 47881429 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/sXuEvDEUW2 -s 69081244 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/sXuEvDEUW2 -s 83459376 .. ok test_bcf_sr_no_index: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr --no-index -p all --args /build/reproducible-path/htslib-1.21+ds/test/bcf-sr/merge.noidx.a.vcf /build/reproducible-path/htslib-1.21+ds/test/bcf-sr/merge.noidx.b.vcf /build/reproducible-path/htslib-1.21+ds/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/sXuEvDEUW2/no_index_1.err .. ok test_bcf_sr_no_index: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr --no-index -p all --args /build/reproducible-path/htslib-1.21+ds/test/bcf-sr/merge.noidx.a.vcf /build/reproducible-path/htslib-1.21+ds/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/sXuEvDEUW2/no_index_2.out 2> /tmp/sXuEvDEUW2/no_index_2.err (expected fail) .. ok test_bcf_sr_no_index: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr --no-index -p all --args /build/reproducible-path/htslib-1.21+ds/test/bcf-sr/merge.noidx.a.vcf /build/reproducible-path/htslib-1.21+ds/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/sXuEvDEUW2/no_index_3.out 2> /tmp/sXuEvDEUW2/no_index_3.err (expected fail) .. ok test_bcf_sr_no_index: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr --no-index -p all --args /build/reproducible-path/htslib-1.21+ds/test/bcf-sr/merge.noidx.rec_order.vcf /build/reproducible-path/htslib-1.21+ds/test/bcf-sr/merge.noidx.a.vcf > /tmp/sXuEvDEUW2/no_index_4.out 2> /tmp/sXuEvDEUW2/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test_view -b -p /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf -x /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf.csi /build/reproducible-path/htslib-1.21+ds/test/bcf-sr/weird-chr-names.vcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_1.out.vcf -r '1' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_2.out.vcf -r '1:1-2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_4.out.vcf -r '1:1-1' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_5.out.vcf -r '{1:1}' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set regions .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_14.out.vcf -t '1' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_15.out.vcf -t '1:1-2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_17.out.vcf -t '1:1-1' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_18.out.vcf -t '{1:1}' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/sXuEvDEUW2/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/sXuEvDEUW2/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set targets .. ok test_command: /build/reproducible-path/htslib-1.21+ds/test/test-bcf-translate - .. ok test_convert_padded_header: /build/reproducible-path/htslib-1.21+ds/test/test_view -t ce.fa -C /tmp/sXuEvDEUW2/headernul0.bam .. ok test_convert_padded_header: /build/reproducible-path/htslib-1.21+ds/test/test_view -t ce.fa -C /tmp/sXuEvDEUW2/headernul1.bam .. ok test_convert_padded_header: /build/reproducible-path/htslib-1.21+ds/test/test_view -t ce.fa -C /tmp/sXuEvDEUW2/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /build/reproducible-path/htslib-1.21+ds/bgzip -I /build/reproducible-path/htslib-1.21+ds/test/bgziptest.txt.tmp.gz.gzi -c -g /build/reproducible-path/htslib-1.21+ds/test/bgziptest.txt .. ok test-logging: /build/reproducible-path/htslib-1.21+ds/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/build/reproducible-path/htslib-1.21+ds /build/reproducible-path/htslib-1.21+ds/test/with-shlib.sh /build/reproducible-path/htslib-1.21+ds/htsfile https://localhost:99999/invalid_port .. ok test_realn: /build/reproducible-path/htslib-1.21+ds/test/test_realn -f /build/reproducible-path/htslib-1.21+ds/test/realn01.fa -i /build/reproducible-path/htslib-1.21+ds/test/realn01.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.21+ds/test/test_realn -f /build/reproducible-path/htslib-1.21+ds/test/realn02.fa -i /build/reproducible-path/htslib-1.21+ds/test/realn02.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.21+ds/test/test_realn -a -f /build/reproducible-path/htslib-1.21+ds/test/realn01.fa -i /build/reproducible-path/htslib-1.21+ds/test/realn01.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.21+ds/test/test_realn -a -f /build/reproducible-path/htslib-1.21+ds/test/realn02.fa -i /build/reproducible-path/htslib-1.21+ds/test/realn02.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.21+ds/test/test_realn -e -f /build/reproducible-path/htslib-1.21+ds/test/realn01.fa -i /build/reproducible-path/htslib-1.21+ds/test/realn01.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.21+ds/test/test_realn -e -f /build/reproducible-path/htslib-1.21+ds/test/realn02.fa -i /build/reproducible-path/htslib-1.21+ds/test/realn02.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.21+ds/test/test_realn -r -f /build/reproducible-path/htslib-1.21+ds/test/realn02.fa -i /build/reproducible-path/htslib-1.21+ds/test/realn02-r.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.21+ds/test/test_realn -a -f /build/reproducible-path/htslib-1.21+ds/test/realn02.fa -i /build/reproducible-path/htslib-1.21+ds/test/realn02_exp.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.21+ds/test/test_realn -f /build/reproducible-path/htslib-1.21+ds/test/realn02.fa -i /build/reproducible-path/htslib-1.21+ds/test/realn02_exp-a.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.21+ds/test/test_realn -f /build/reproducible-path/htslib-1.21+ds/test/realn03.fa -e -i /build/reproducible-path/htslib-1.21+ds/test/realn03.sam -o - .. ok test-bcf_set_variant_type: /build/reproducible-path/htslib-1.21+ds/test/test-bcf_set_variant_type .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap --allow-dups -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap --allow-dups -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap --allow-dups -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -c chr,beg,end -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl,value:overlap,value -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl,value:overlap,value -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl,value:overlap,value -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -O 0.5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -O 0.5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -O 0.5 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -rO 0.5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -rO 0.5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -rO 0.5 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.2.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -a nbp,frac -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.3.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.3.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -a nbp,frac -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.3.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.3.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl:overlap -a nbp,frac -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.4.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.4.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.4.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.4.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.5.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.5.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.5.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.5.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.6.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.6.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.6.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.6.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.7.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.7.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.7.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.7.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.8.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.8.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.8.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.8.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.9.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.9.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.9.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.9.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -f smpl -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -x -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -x -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -x -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -m smpl -f smpl -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -m smpl -f smpl -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -m smpl -f smpl -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -m smpl -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -m smpl -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -m smpl -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -m smpl -x -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -m smpl -x -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.10.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -m smpl -x -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.12.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.12.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.12.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.12.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.12.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -t /build/reproducible-path/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok Number of tests: total .. 340 passed .. 340 failed .. 0 make[2]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' rm -fr -- /tmp/dh-xdg-rundir-YZe5VAQe make[1]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/reproducible-path/htslib-1.21+ds' echo "Suppress test for Architecture independant builds." Suppress test for Architecture independant builds. make[1]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/libhts3t64.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars rm -fr -- debian/.debhelper/generated/libhts3t64/ debian/libhts3t64/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/htslib-test/ debian/htslib-test/ debian/.debhelper/generated/tabix/ debian/tabix/ debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/htslib-1.21+ds' for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \ rm /build/reproducible-path/htslib-1.21+ds/test/${binary} ; \ done dh_auto_install -- prefix=/usr \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.21" \ libdir=/usr/lib/arm-linux-gnueabihf install -m0755 -d /build/reproducible-path/htslib-1.21\+ds/debian/tmp make -j4 install DESTDIR=/build/reproducible-path/htslib-1.21\+ds/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.21 libdir=/usr/lib/arm-linux-gnueabihf make[2]: Entering directory '/build/reproducible-path/htslib-1.21+ds' mkdir -p -m 755 /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/bin /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/include /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/include/htslib /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/lib/arm-linux-gnueabihf /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/share/man/man1 /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/share/man/man5 /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/share/man/man7 /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig if test -n "/usr/lib/arm-linux-gnueabihf/htslib"; then mkdir -p -m 755 /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/htslib; fi install -p -m 644 libhts.so /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.21 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/arm-linux-gnueabihf#g;s#@-PACKAGE_VERSION@#1.21#g' htslib.pc.tmp > /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc ln -sf libhts.so.1.21 /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so ln -sf libhts.so.1.21 /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3 chmod 644 /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc install -p annot-tsv bgzip htsfile tabix /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/htslib; fi install -p -m 644 htslib/*.h /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/include/htslib install -p -m 644 libhts.a /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /build/reproducible-path/htslib-1.21+ds/debian/tmp/usr/share/man/man7 make[2]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' # restore clean copy of test dir before dh_install is run # This should not be done earlier since dh_auto_install contains some unconditional removals rm -f -r test mv test_backup test make[1]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/htslib-1.21+ds' dh_install --indep install -m0755 -d debian/htslib-test/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/tests/run-unit-test debian/htslib-test/usr/share/doc/libhts-dev/ install -m0755 -d debian/htslib-test/usr/share/htslib-test cp --reflink=auto -a ./Makefile ./annot-tsv.c ./bcf_sr_sort.c ./bcf_sr_sort.h ./bgzf.c ./bgzip.c ./config.h ./config.mk ./config_vars.h ./errmod.c ./faidx.c ./fuzz_settings.h ./header.c ./header.h ./hfile.c ./hfile_gcs.c ./hfile_internal.h ./hfile_libcurl.c ./hfile_s3.c ./hfile_s3_write.c ./hts.c ./hts_expr.c ./hts_internal.h ./hts_os.c ./hts_time_funcs.h ./htscodecs.mk ./htscodecs_bundled.mk ./htscodecs_external.mk ./htsfile.c ./htslib.mk ./htslib_static.mk ./htslib_vars.mk ./kfunc.c ./kstring.c ./md5.c ./multipart.c ./os ./plugin.c ./probaln.c ./realn.c ./regidx.c ./region.c ./sam.c ./sam_internal.h ./sam_mods.c ./simd.c ./synced_bcf_reader.c ./tabix.c ./tbx.c ./textutils.c ./textutils_internal.h ./thread_pool.c ./thread_pool_internal.h ./vcf.c ./vcf_sweep.c ./vcfutils.c ./version.h ./version.sh debian/htslib-test/usr/share/htslib-test/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/cram cp --reflink=auto -a ./cram/cram.h ./cram/cram_codecs.c ./cram/cram_codecs.h ./cram/cram_decode.c ./cram/cram_decode.h ./cram/cram_encode.c ./cram/cram_encode.h ./cram/cram_external.c ./cram/cram_index.c ./cram/cram_index.h ./cram/cram_io.c ./cram/cram_io.h ./cram/cram_samtools.h ./cram/cram_stats.c ./cram/cram_stats.h ./cram/cram_structs.h ./cram/mFILE.c ./cram/mFILE.h ./cram/misc.h ./cram/open_trace_file.c ./cram/open_trace_file.h ./cram/os.h ./cram/pooled_alloc.c ./cram/pooled_alloc.h ./cram/string_alloc.c ./cram/string_alloc.h debian/htslib-test/usr/share/htslib-test/cram/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/test cp --reflink=auto -a ./test/annot-tsv ./test/auxf\#values.sam ./test/auxf\#values_java.cram ./test/auxf.fa ./test/auxf.fa.fai ./test/base_mods ./test/bcf-sr ./test/bgzf_boundaries ./test/bgziptest.txt ./test/bgziptest.txt.gz ./test/bgziptest.txt.gz.gzi ./test/c1\#bounds.sam ./test/c1\#clip.sam ./test/c1\#noseq.sam ./test/c1\#pad1.sam ./test/c1\#pad2.sam ./test/c1\#pad3.sam ./test/c1\#unknown.sam ./test/c1.fa ./test/c1.fa.fai ./test/c2\#pad.sam ./test/c2.fa ./test/c2.fa.fai ./test/ce\#1.sam ./test/ce\#1000.sam ./test/ce\#2.sam ./test/ce\#5.sam ./test/ce\#5b.sam ./test/ce\#5b_java.cram ./test/ce\#large_seq.sam ./test/ce\#supp.sam ./test/ce\#tag_depadded.sam ./test/ce\#tag_padded.sam ./test/ce\#unmap.sam ./test/ce\#unmap1.sam ./test/ce\#unmap2.sam ./test/ce.fa ./test/ce.fa.fai ./test/colons.bam ./test/colons.bam.bai ./test/compare_sam.pl ./test/cross_validate.sh ./test/emptyfile ./test/faidx ./test/fastq ./test/fastqs_README.txt ./test/fieldarith.c ./test/fieldarith.sam ./test/formatcols.vcf ./test/formatmissing-out.vcf ./test/formatmissing.vcf ./test/fuzz ./test/header_syms.pl ./test/hfile.c ./test/hts_endian.c ./test/index.bam.bai ./test/index.bam.csi ./test/index.bcf.csi ./test/index.cram.crai ./test/index.sam ./test/index.sam.gz.bai ./test/index.sam.gz.csi ./test/index.vcf ./test/index.vcf.gz.csi ./test/index.vcf.gz.tbi ./test/index2.sam ./test/index_dos.sam ./test/longrefs ./test/maintainer ./test/md\#1.sam ./test/md.fa ./test/md.fa.fai ./test/modhdr.expected.vcf ./test/modhdr.vcf.gz ./test/modhdr.vcf.gz.csi ./test/mpileup ./test/no_hdr_sq_1.bam ./test/no_hdr_sq_1.bam.csi ./test/no_hdr_sq_1.expected.sam ./test/noroundtrip-out.vcf ./test/noroundtrip.vcf ./test/pileup.c ./test/pileup_mod.c ./test/plugins-dlhts.c ./test/range.bam ./test/range.bam.bai ./test/range.cram ./test/range.cram.crai ./test/range.out ./test/range.out2 ./test/realn01.fa ./test/realn01.fa.fai ./test/realn01.sam ./test/realn01_exp-a.sam ./test/realn01_exp-e.sam ./test/realn01_exp.sam ./test/realn02-r.sam ./test/realn02.fa ./test/realn02.fa.fai ./test/realn02.sam ./test/realn02_exp-a.sam ./test/realn02_exp-e.sam ./test/realn02_exp.sam ./test/realn03.fa ./test/realn03.fa.fai ./test/realn03.sam ./test/realn03_exp.sam ./test/sam.c ./test/sam_filter ./test/simple_test_driver.sh ./test/tabix ./test/tabix.out ./test/test-bcf-sr.c ./test/test-bcf-sr.pl ./test/test-bcf-translate.c ./test/test-bcf-translate.out ./test/test-bcf_set_variant_type.c ./test/test-logging.pl ./test/test-parse-reg.c ./test/test-regidx.c ./test/test-vcf-api.c ./test/test-vcf-api.out ./test/test-vcf-hdr-in.vcf ./test/test-vcf-hdr.out ./test/test-vcf-sweep.c ./test/test-vcf-sweep.out ./test/test.pl ./test/test_bgzf.c ./test/test_expr.c ./test/test_faidx.c ./test/test_index.c ./test/test_introspection.c ./test/test_kfunc.c ./test/test_khash.c ./test/test_kstring.c ./test/test_mod.c ./test/test_nibbles.c ./test/test_realn.c ./test/test_str2int.c ./test/test_time_funcs.c ./test/test_view.c ./test/thrash_threads1.c ./test/thrash_threads2.c ./test/thrash_threads3.c ./test/thrash_threads4.c ./test/thrash_threads5.c ./test/thrash_threads6.c ./test/thrash_threads7.c ./test/thread_pool.md ./test/usepublic.cpp ./test/vcf_meta_meta.vcf ./test/with-shlib.sh ./test/xx\#MD.sam ./test/xx\#MD2.sam ./test/xx\#blank.sam ./test/xx\#large_aux.sam ./test/xx\#large_aux2.sam ./test/xx\#large_aux_java.cram ./test/xx\#minimal.sam ./test/xx\#pair.sam ./test/xx\#repeated.sam ./test/xx\#rg.sam ./test/xx\#tlen.sam ./test/xx\#tlen2.sam ./test/xx\#triplet.sam ./test/xx\#unsorted.sam ./test/xx.fa ./test/xx.fa.fai debian/htslib-test/usr/share/htslib-test/test/ sed -i 's/-ffile-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk sed -i 's/-fdebug-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk sed -i 's#\.\./\.\./htslib/#htslib/#' `grep -Rl '../../htslib/' debian/htslib-test/*` make[1]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' dh_install -Nhtslib-test install -m0755 -d debian/libhts3t64/usr/lib/arm-linux-gnueabihf cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/htslib debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.21 debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3 debian/libhts3t64/usr/lib/arm-linux-gnueabihf/ install -m0755 -d debian/libhts3t64/usr/share/man/man5 cp --reflink=auto -a debian/tmp/usr/share/man/man5/faidx.5 debian/tmp/usr/share/man/man5/sam.5 debian/tmp/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man5/ install -m0755 -d debian/libhts-dev/usr/include cp --reflink=auto -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/ install -m0755 -d debian/libhts-dev/usr/lib/arm-linux-gnueabihf cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so debian/libhts-dev/usr/lib/arm-linux-gnueabihf/ install -m0755 -d debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig/ install -m0755 -d debian/tabix/usr/bin cp --reflink=auto -a ./bgzip ./htsfile ./tabix debian/tabix/usr/bin/ rm -f debian/htslib-test.debhelper.log debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/htslib-1.21+ds' dh_installdocs install -m0755 -d debian/libhts3t64/usr/share/doc/libhts3t64 install -p -m0644 debian/copyright debian/libhts3t64/usr/share/doc/libhts3t64/copyright install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/README.test debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README.large_positions.md debian/libhts-dev/usr/share/doc/libhts-dev chmod -R u\+rw,go=rX debian/libhts-dev/usr/share/doc install -p -m0644 debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/copyright debian/htslib-test/usr/share/doc/htslib-test/copyright install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright # Fix Perl interpreter path for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so: No such file or directory make[1]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/htslib-1.21+ds' dh_installchangelogs NEWS install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -p -m0644 debian/.debhelper/generated/libhts-dev/dh_installchangelogs.dch.trimmed debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/.debhelper/generated/tabix/dh_installchangelogs.dch.trimmed debian/tabix/usr/share/doc/tabix/changelog.Debian install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog install -m0755 -d debian/libhts3t64/usr/share/doc/libhts3t64 install -p -m0644 debian/.debhelper/generated/libhts3t64/dh_installchangelogs.dch.trimmed debian/libhts3t64/usr/share/doc/libhts3t64/changelog.Debian install -p -m0644 NEWS debian/libhts3t64/usr/share/doc/libhts3t64/changelog install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/.debhelper/generated/htslib-test/dh_installchangelogs.dch.trimmed debian/htslib-test/usr/share/doc/htslib-test/changelog.Debian install -p -m0644 NEWS debian/htslib-test/usr/share/doc/htslib-test/changelog make[1]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' dh_installman install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./htsfile.1 debian/tabix/usr/share/man/man1/htsfile.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./tabix.1 debian/tabix/usr/share/man/man1/tabix.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./bgzip.1 debian/tabix/usr/share/man/man1/bgzip.1 install -m0755 -d debian/libhts3t64/usr/share/man/man7/ install -p -m0644 ./htslib-s3-plugin.7 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3t64/usr/share/man/man5/faidx.5 debian/libhts3t64/usr/share/man/man5/sam.5 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/tabix.1 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3t64/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1 mv debian/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1 chmod 0644 -- debian/tabix/usr/share/man/man1/tabix.1 mv debian/libhts3t64/usr/share/man/man5/faidx.5.dh-new debian/libhts3t64/usr/share/man/man5/faidx.5 mv debian/libhts3t64/usr/share/man/man5/sam.5.dh-new debian/libhts3t64/usr/share/man/man5/sam.5 chmod 0644 -- debian/libhts3t64/usr/share/man/man5/faidx.5 debian/libhts3t64/usr/share/man/man5/sam.5 mv debian/libhts3t64/usr/share/man/man5/vcf.5.dh-new debian/libhts3t64/usr/share/man/man5/vcf.5 mv debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 chmod 0644 -- debian/libhts3t64/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 mv debian/tabix/usr/share/man/man1/bgzip.1.dh-new debian/tabix/usr/share/man/man1/bgzip.1 mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1 chmod 0644 -- debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1 dh_lintian install -m0755 -d debian/libhts-dev/usr/share/lintian/overrides install -p -m0644 debian/libhts-dev.lintian-overrides debian/libhts-dev/usr/share/lintian/overrides/libhts-dev install -m0755 -d debian/htslib-test/usr/share/lintian/overrides install -p -m0644 debian/htslib-test.lintian-overrides debian/htslib-test/usr/share/lintian/overrides/htslib-test dh_perl mv debian/htslib-test.substvars.new debian/htslib-test.substvars dh_link rm -f debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.3 ln -s libhts.so.1.21 debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.3 rm -f debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so ln -s libhts.so.1.21 debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so rm -f debian/htslib-test/usr/share/htslib-test/htscodecs.mk ln -s htscodecs_external.mk debian/htslib-test/usr/share/htslib-test/htscodecs.mk install -m0755 -d debian/tabix/usr/share/man/man1 rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz ln -s tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz dh_strip_nondeterminism dh_compress cd debian/htslib-test cd debian/libhts3t64 cd debian/libhts-dev cd debian/tabix chmod a-x usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 gzip -9nf usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian chmod a-x usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 chmod a-x usr/share/doc/libhts3t64/changelog usr/share/doc/libhts3t64/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 gzip -9nf usr/share/doc/libhts3t64/changelog usr/share/doc/libhts3t64/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 gzip -9nf usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian cd '/build/reproducible-path/htslib-1.21+ds' cd '/build/reproducible-path/htslib-1.21+ds' cd '/build/reproducible-path/htslib-1.21+ds' cd '/build/reproducible-path/htslib-1.21+ds' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/htslib-1.21+ds' dh_fixperms find debian/tabix ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/htslib-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts3t64 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/doc -type f -a -true -a ! -regex 'debian/htslib-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts3t64/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/htslib-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts-dev/usr/include debian/libhts-dev/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/htslib-test/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/htslib-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian -name simple_test_driver.sh -exec chmod +x \{\} \; make[1]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/htslib-1.21+ds' # FIXME: No idea why these files are remaining in debian/tmp rm -rf debian/tmp/usr/bin debian/tmp/usr/share/man dh_missing make[1]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' dh_dwz -a install -m0755 -d debian/libhts3t64/usr/lib/debug/.dwz/arm-linux-gnueabihf dwz -mdebian/libhts3t64/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3t64.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3t64.debug -- debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.21 install -m0755 -d debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf dwz -mdebian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix dwz: debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so: DWARF compression not beneficial - old size 36226 new size 36291 dwz: debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.21: DWARF compression not beneficial - old size 866436 new size 886239 objcopy --compress-debug-sections debian/libhts3t64/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3t64.debug chmod 0644 -- debian/libhts3t64/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3t64.debug objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug chmod 0644 -- debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_strip make[1]: Entering directory '/build/reproducible-path/htslib-1.21+ds' # This is apparently important for the interpretation by ldc2 in sambamba dh_strip -Xlibhts.a install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/85 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.21 debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/85/c56585f999aa03680025d3c803fd7acd9766cc.debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/8c objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/8c/95eba028592946e131086f7d051d33e2f01ea7.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/8c/95eba028592946e131086f7d051d33e2f01ea7.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/htsfile objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/8c/95eba028592946e131086f7d051d33e2f01ea7.debug debian/tabix/usr/bin/htsfile install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e4 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e4/243795de56e2d939b093076ee3ba5a737183d2.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/85/c56585f999aa03680025d3c803fd7acd9766cc.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.21 objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/85/c56585f999aa03680025d3c803fd7acd9766cc.debug debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.21 install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/6a objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/6a/6c0a9e664db8384ed1b12f579d20418f745b97.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/6a/6c0a9e664db8384ed1b12f579d20418f745b97.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/6a/6c0a9e664db8384ed1b12f579d20418f745b97.debug debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/5c objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/5c/1fcf0c4b3cc927e5cc41aa8844dad00461e015.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/5c/1fcf0c4b3cc927e5cc41aa8844dad00461e015.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/5c/1fcf0c4b3cc927e5cc41aa8844dad00461e015.debug debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/49 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/49/3f8c0e807cdf7a030ff5d691cb9460731e1541.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e4/243795de56e2d939b093076ee3ba5a737183d2.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e4/243795de56e2d939b093076ee3ba5a737183d2.debug debian/tabix/usr/bin/bgzip chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/49/3f8c0e807cdf7a030ff5d691cb9460731e1541.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/49/3f8c0e807cdf7a030ff5d691cb9460731e1541.debug debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c7 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c7/5858aa6244617a85f7667dbb57e9cdb720eef2.debug install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/27 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/27/232750f38054f198897b01dc960dadfe24a28b.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/27/232750f38054f198897b01dc960dadfe24a28b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/27/232750f38054f198897b01dc960dadfe24a28b.debug debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/libhts3t64/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/libhts3t64/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/libhts3t64/usr/lib/debug install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/share/doc ln -s libhts3t64 debian/.debhelper/libhts3t64/dbgsym-root/usr/share/doc/libhts3t64-dbgsym install -m0755 -d debian/.debhelper/libhts3t64 chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c7/5858aa6244617a85f7667dbb57e9cdb720eef2.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/tabix objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c7/5858aa6244617a85f7667dbb57e9cdb720eef2.debug debian/tabix/usr/bin/tabix install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/tabix/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/tabix/usr/lib/debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym install -m0755 -d debian/.debhelper/tabix make[1]: Leaving directory '/build/reproducible-path/htslib-1.21+ds' dh_makeshlibs -a rm -f debian/libhts3t64/DEBIAN/shlibs install -m0755 -d debian/libhts3t64/DEBIAN echo "libhts 3 libhts3t64 (>= 1.21+ds)" >> debian/libhts3t64/DEBIAN/shlibs chmod 0644 -- debian/libhts3t64/DEBIAN/shlibs dpkg-gensymbols -plibhts3t64 -Idebian/libhts3t64.symbols -Pdebian/libhts3t64 -edebian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.21 mv debian/.debhelper/generated/libhts3t64/triggers.new debian/.debhelper/generated/libhts3t64/triggers echo t64:Provides= >> debian/libhts3t64.substvars rm -f debian/libhts-dev/DEBIAN/shlibs rm -f debian/tabix/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/libhts3t64/DEBIAN dpkg-shlibdeps -Tdebian/libhts3t64.substvars debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.21 debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so install -m0755 -d debian/tabix/DEBIAN dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/tabix dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dh_installdeb install -m0755 -d debian/libhts3t64/DEBIAN install -p -m0644 debian/.debhelper/generated/libhts3t64/triggers debian/libhts3t64/DEBIAN/triggers install -m0755 -d debian/libhts-dev/DEBIAN install -m0755 -d debian/htslib-test/DEBIAN install -m0755 -d debian/tabix/DEBIAN dh_gencontrol install -m0755 -d debian/tabix/DEBIAN echo misc:Depends= >> debian/tabix.substvars echo misc:Pre-Depends= >> debian/tabix.substvars install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -cdebian/control -Pdebian/.debhelper/tabix/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=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=8c95eba028592946e131086f7d051d33e2f01ea7 c75858aa6244617a85f7667dbb57e9cdb720eef2 e4243795de56e2d939b093076ee3ba5a737183d2" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/libhts3t64/DEBIAN echo misc:Depends= >> debian/libhts3t64.substvars echo misc:Pre-Depends= >> debian/libhts3t64.substvars install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -cdebian/control -Pdebian/.debhelper/libhts3t64/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=libhts3t64-dbgsym "-DDepends=libhts3t64 (= \${binary:Version})" "-DDescription=debug symbols for libhts3t64" "-DBuild-Ids=27232750f38054f198897b01dc960dadfe24a28b 493f8c0e807cdf7a030ff5d691cb9460731e1541 5c1fcf0c4b3cc927e5cc41aa8844dad00461e015 6a6c0a9e664db8384ed1b12f579d20418f745b97 85c56585f999aa03680025d3c803fd7acd9766cc" -DSection=debug -UReplaces -UBreaks install -m0755 -d debian/htslib-test/DEBIAN echo misc:Depends= >> debian/htslib-test.substvars echo misc:Pre-Depends= >> debian/htslib-test.substvars dpkg-gencontrol -phtslib-test -ldebian/changelog -Tdebian/htslib-test.substvars -cdebian/control -Pdebian/htslib-test install -m0755 -d debian/libhts-dev/DEBIAN echo misc:Depends= >> debian/libhts-dev.substvars echo misc:Pre-Depends= >> debian/libhts-dev.substvars dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -cdebian/control -Pdebian/libhts-dev chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -cdebian/control -Pdebian/libhts3t64 chmod 0644 -- debian/libhts-dev/DEBIAN/control chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -cdebian/control -Pdebian/tabix chmod 0644 -- debian/htslib-test/DEBIAN/control chmod 0644 -- debian/libhts3t64/DEBIAN/control chmod 0644 -- debian/tabix/DEBIAN/control dh_md5sums install -m0755 -d debian/tabix/DEBIAN install -m0755 -d debian/libhts3t64/DEBIAN cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/libhts-dev/DEBIAN cd debian/libhts3t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/htslib-test/DEBIAN cd debian/htslib-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts3t64/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN chmod 0644 -- debian/tabix/DEBIAN/md5sums install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN cd debian/.debhelper/libhts3t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums chmod 0644 -- debian/htslib-test/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/libhts3t64 .. dpkg-deb --root-owner-group --build debian/libhts-dev .. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.21+ds-0+exp2_armhf.deb'. dpkg-deb: building package 'libhts3t64' in '../libhts3t64_1.21+ds-0+exp2_armhf.deb'. dpkg-deb --root-owner-group --build debian/tabix .. dpkg-deb: building package 'tabix' in '../tabix_1.21+ds-0+exp2_armhf.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/libhts3t64/dbgsym-root .. dpkg-deb: building package 'libhts3t64-dbgsym' in '../libhts3t64-dbgsym_1.21+ds-0+exp2_armhf.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root .. dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.21+ds-0+exp2_armhf.deb'. dpkg-deb --root-owner-group --build debian/htslib-test .. dpkg-deb: building package 'htslib-test' in '../htslib-test_1.21+ds-0+exp2_all.deb'. dpkg-genbuildinfo --build=binary -O../htslib_1.21+ds-0+exp2_armhf.buildinfo dpkg-genchanges --build=binary -O../htslib_1.21+ds-0+exp2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from htslib-1.21+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/14935/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/14935/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/14935 and its subdirectories I: Current time: Thu Nov 21 15:48:11 +14 2024 I: pbuilder-time-stamp: 1732153691