Mon Jan 8 20:10:22 UTC 2024 I: starting to build htslib/bullseye/armhf on jenkins on '2024-01-08 20:10' Mon Jan 8 20:10:22 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_5/7995/console.log Mon Jan 8 20:10:22 UTC 2024 I: Downloading source for bullseye/htslib=1.11-4 --2024-01-08 20:10:22-- http://cdn-fastly.deb.debian.org/debian/pool/main/h/htslib/htslib_1.11-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2329 (2.3K) [text/prs.lines.tag] Saving to: ‘htslib_1.11-4.dsc’ 0K .. 100% 158M=0s 2024-01-08 20:10:23 (158 MB/s) - ‘htslib_1.11-4.dsc’ saved [2329/2329] Mon Jan 8 20:10:23 UTC 2024 I: htslib_1.11-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: htslib Binary: libhts3, libhts-dev, htslib-test, tabix Architecture: any all Version: 1.11-4 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Michael R. Crusoe , Steffen Moeller Homepage: https://github.com/samtools/htslib Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/htslib Vcs-Git: https://salsa.debian.org/med-team/htslib.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, build-essential Build-Depends: debhelper-compat (= 13), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev Package-List: htslib-test deb science optional arch=all libhts-dev deb libdevel optional arch=any libhts3 deb libs optional arch=any tabix deb science optional arch=any Checksums-Sha1: 815b8268bfd6526c2d5fc639f5e6f7ed264dcbf7 1333118 htslib_1.11.orig.tar.bz2 15aba4a37194c0db94a8c86dba0dd15769270793 17096 htslib_1.11-4.debian.tar.xz Checksums-Sha256: cffadd9baa6fce27b8fe0b01a462b489f06a5433dfe92121f667f40f632538d7 1333118 htslib_1.11.orig.tar.bz2 0e96663ceda766d8dd78b476e196c214c6e3c05fbe02d8f1d56191daa65df370 17096 htslib_1.11-4.debian.tar.xz Files: c488c7a79283e5252c04cae335ee80e8 1333118 htslib_1.11.orig.tar.bz2 1e6778e704926fe2398f7caa571cb24b 17096 htslib_1.11-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl/wkS8ACgkQPCZ2P2xn 5uJPIhAAx9hf8NelyFn35HQcjeuc2hyb+TMmBwpA35HRgRT6TW+7c9UZEFSgVpf3 1ehWCl2C4gUq4d49hd6Ljq3Wk9LDwYXbiYF8VHuJYrX2hQnflnQELhpG1KQrtxKa LOyJvutqWnY5LXHmsraAXnK48DJGk+wj2UUB8Geld9JXagpg2X/OujBIV4H2qX1n ZsCZD2VJ17BVvQ0mwUMSTFM4BXD987iMd6PzpLy1nb9EroTTOU/LMEiSyLJUln12 wyOp45rxL+m7gDcw8Wy3nk16lxSrID8G2T4SsSfygmgAJJOOhzDxLii2R1Uow3e5 xewGFWqAH457wvFxsW3oT197ePYFNU9jhtRSFa/FrhQW6O5P/gneOqrfINgR4t6v MUXkcpAQNJ9KtHUBqZ1nTz9RyBJ/FQY73s76ZN0FDUa2DIYBc1z6inmMMw2o8JMt LSF+n/IlPcB4wiNiYUFTpRQxLnwAjyGsF9/ATotcmI7B0l86YN1toRWyfr5nrLnr 4VlgBeyrsZIDJBO177tHgEOxDoDXzClvdNNENBAE5ILqJkaOOyPzFYYEHXsJsk/T +Nq1CuVjaA7TNWOktczOb6BMMNVdZnjkfgo3FUUvhDe08RJ501CKK6WYat7wEaNp we4wcXBJoaofsYYYPy2Oi5+MxrShxZijlqKZX8xkSoQTtLiomh4= =wBH4 -----END PGP SIGNATURE----- Mon Jan 8 20:10:23 UTC 2024 I: Checking whether the package is not for us Mon Jan 8 20:10:23 UTC 2024 I: Starting 1st build on remote node virt64a-armhf-rb.debian.net. Mon Jan 8 20:10:23 UTC 2024 I: Preparing to do remote build '1' on virt64a-armhf-rb.debian.net. Mon Jan 8 20:23:40 UTC 2024 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 8 08:10:30 -12 2024 I: pbuilder-time-stamp: 1704744630 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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_1.11-4.dsc] I: copying [./htslib_1.11.orig.tar.bz2] I: copying [./htslib_1.11-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.AFJJIspM/trustedkeys.kbx': General error gpgv: Signature made Sat Jan 2 15:28:47 2021 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./htslib_1.11-4.dsc dpkg-source: info: extracting htslib in htslib-1.11 dpkg-source: info: unpacking htslib_1.11.orig.tar.bz2 dpkg-source: info: unpacking htslib_1.11-4.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 cram_to_bam_export.patch dpkg-source: info: applying 273c5e76a1694aa2a13fd51c133abed2ef8ab4d3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/15890/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='c040a863a2c340b7a91c509fc04853e3' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='15890' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.gzc3bV7t/pbuilderrc_CiUe --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gzc3bV7t/b1 --logfile b1/build.log htslib_1.11-4.dsc' SUDO_GID='114' SUDO_UID='108' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64a 6.1.0-17-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Mar 27 2022 bash -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash -rwxr-xr-x 1 root root 75880 Sep 22 2020 date -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd -rwxr-xr-x 1 root root 59912 Sep 22 2020 df -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir -rwxr-xr-x 1 root root 55012 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 22496 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 47492 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 26076 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 124508 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 64212 Apr 10 2022 gzip -rwxr-xr-x 1 root root 13784 Nov 7 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln -rwxr-xr-x 1 root root 35068 Feb 7 2020 login -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls -rwxr-xr-x 1 root root 99940 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 34408 Jan 20 2022 more -rwsr-xr-x 1 root root 34400 Jan 20 2022 mount -rwxr-xr-x 1 root root 9824 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 7 09:29 sh -> dash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Jan 20 2022 su -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync -rwxr-xr-x 1 root root 340872 Feb 17 2021 tar -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch -rwxr-xr-x 1 root root 22496 Sep 22 2020 true -rwxr-xr-x 1 root root 9636 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 22108 Jan 20 2022 umount -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir -rwxr-xr-x 1 root root 38512 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/15890/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: debhelper-compat (= 13), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 17486 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 dh-exec; however: Package dh-exec 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. 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} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{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 libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 21.5 MB of archives. After unpacking 73.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8+deb11u1 [139 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3+deb11u1 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3+deb11u1 [120 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3+deb11u1 [68.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7+deb11u4 [602 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf dh-exec armhf 0.23.2 [25.1 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf libbrotli1 armhf 1.0.9-2+b2 [262 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libbz2-dev armhf 1.0.8-4 [29.2 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2.1+deb11u1 [67.7 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf libsasl2-2 armhf 2.1.27+dfsg-2.1+deb11u1 [99.2 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf libldap-2.4-2 armhf 2.4.57+dfsg-3+deb11u1 [210 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf libnghttp2-14 armhf 1.43.0-1 [65.6 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf libpsl5 armhf 0.21.0-1.2 [56.1 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf libssh2-1 armhf 1.9.0-2 [143 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf libcurl3-gnutls armhf 7.74.0-1.3+deb11u9 [311 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3+deb11u9 [408 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf libdeflate0 armhf 1.7-1 [43.1 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf libdeflate-dev armhf 1.7-1 [39.9 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf liblzma-dev armhf 5.2.5-2.1~deb11u1 [220 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf libssl-dev armhf 1.1.1w-0+deb11u1 [1616 kB] Get: 48 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2+deb11u2 [185 kB] Fetched 21.5 MB in 1s (18.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17486 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_armhf.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3+deb11u1_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3+deb11u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../07-libmagic1_1%3a5.39-3+deb11u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.39-3+deb11u1) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3+deb11u1_armhf.deb ... Unpacking file (1:5.39-3+deb11u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_armhf.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../10-libsigsegv2_2.13-1_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_armhf.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../23-libelf1_0.183-1_armhf.deb ... Unpacking libelf1:armhf (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_armhf.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:armhf. Preparing to unpack .../25-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7+deb11u4_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package dh-exec. Preparing to unpack .../31-dh-exec_0.23.2_armhf.deb ... Unpacking dh-exec (0.23.2) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../32-libbrotli1_1.0.9-2+b2_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b2) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../33-libbz2-dev_1.0.8-4_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.8-4) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../34-libsasl2-modules-db_2.1.27+dfsg-2.1+deb11u1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../35-libsasl2-2_2.1.27+dfsg-2.1+deb11u1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libldap-2.4-2:armhf. Preparing to unpack .../36-libldap-2.4-2_2.4.57+dfsg-3+deb11u1_armhf.deb ... Unpacking libldap-2.4-2:armhf (2.4.57+dfsg-3+deb11u1) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../37-libnghttp2-14_1.43.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.43.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../38-libpsl5_0.21.0-1.2_armhf.deb ... Unpacking libpsl5:armhf (0.21.0-1.2) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../39-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../40-libssh2-1_1.9.0-2_armhf.deb ... Unpacking libssh2-1:armhf (1.9.0-2) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../41-libcurl3-gnutls_7.74.0-1.3+deb11u9_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.74.0-1.3+deb11u9) ... Selecting previously unselected package libcurl4-gnutls-dev:armhf. Preparing to unpack .../42-libcurl4-gnutls-dev_7.74.0-1.3+deb11u9_armhf.deb ... Unpacking libcurl4-gnutls-dev:armhf (7.74.0-1.3+deb11u9) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../43-libdeflate0_1.7-1_armhf.deb ... Unpacking libdeflate0:armhf (1.7-1) ... Selecting previously unselected package libdeflate-dev:armhf. Preparing to unpack .../44-libdeflate-dev_1.7-1_armhf.deb ... Unpacking libdeflate-dev:armhf (1.7-1) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../45-liblzma-dev_5.2.5-2.1~deb11u1_armhf.deb ... Unpacking liblzma-dev:armhf (5.2.5-2.1~deb11u1) ... Selecting previously unselected package libssl-dev:armhf. Preparing to unpack .../46-libssl-dev_1.1.1w-0+deb11u1_armhf.deb ... Unpacking libssl-dev:armhf (1.1.1w-0+deb11u1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../47-zlib1g-dev_1%3a1.2.11.dfsg-2+deb11u2_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2+deb11u2) ... Setting up libpipeline1:armhf (1.5.3-1) ... Setting up libpsl5:armhf (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:armhf (67.1-7) ... Setting up libmagic-mgc (1:5.39-3+deb11u1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:armhf (1.0.9-2+b2) ... Setting up libnghttp2-14:armhf (1.43.0-1) ... Setting up libmagic1:armhf (1:5.39-3+deb11u1) ... Setting up libdeflate0:armhf (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3+deb11u1) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2.1+deb11u1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libsigsegv2:armhf (2.13-1) ... Setting up libssl-dev:armhf (1.1.1w-0+deb11u1) ... Setting up autopoint (0.21-4) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2.1+deb11u1) ... Setting up liblzma-dev:armhf (5.2.5-2.1~deb11u1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2+deb11u2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:armhf (1.9.0-2) ... Setting up libdeflate-dev:armhf (1.7-1) ... Setting up libelf1:armhf (0.183-1) ... Setting up libxml2:armhf (2.9.10+dfsg-6.7+deb11u4) ... Setting up libbz2-dev:armhf (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libldap-2.4-2:armhf (2.4.57+dfsg-3+deb11u1) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:armhf (7.74.0-1.3+deb11u9) ... Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.3+deb11u9) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Setting up dh-exec (0.23.2) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... 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: Running cd /build/reproducible-path/htslib-1.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../htslib_1.11-4_source.changes dpkg-buildpackage: info: source package htslib dpkg-buildpackage: info: source version 1.11-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from htslib-1.11/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-1.11' dh_auto_clean install -d /build/reproducible-path/htslib-1.11/debian/.debhelper/generated/_source/home make -j3 distclean make[2]: Entering directory '/build/reproducible-path/htslib-1.11' rm -f test/*.tmp test/*.tmp.* test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL* header-exports.txt shlib-exports-so.txt rm -f libhts.so libhts.so.* rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h rm -f hts-object-files rm -f libhts.a bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/plugins-dlhts test/sam test/test_bgzf test/test_kfunc test/test_kstring test/test_realn test/test-regidx test/test_str2int 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/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7 rm -f config.cache config.h config.log config.mk config.status rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk rm -rf autom4te.cache make[2]: Leaving directory '/build/reproducible-path/htslib-1.11' rm -rf test_backup/ make[1]: Leaving directory '/build/reproducible-path/htslib-1.11' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/libhts3.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files rm -fr -- debian/libhts3/ 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 \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config 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-1.11' # 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='/htslib' --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:' install -d /build/reproducible-path/htslib-1.11/debian/.debhelper/generated/_source/home ./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=/htslib --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for pkg-config... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking shared library type for unknown-Linux... plain .so checking whether the compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -E checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... (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 library containing dlsym... -ldl 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 libdeflate.h... yes checking for libdeflate_deflate_compress in -ldeflate... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/htslib-1.11' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/htslib-1.11' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \ PACKAGE_VERSION="1.11-4" \ libdir=/usr/lib/arm-linux-gnueabihf make -j3 "CFLAGS=-g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden" PACKAGE_VERSION=1.11-4 libdir=/usr/lib/arm-linux-gnueabihf make[2]: Entering directory '/build/reproducible-path/htslib-1.11' gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION_TEXT "1.11-4"' > version.h gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o plugin.o plugin.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o knetfile.pico knetfile.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_net.pico hfile_net.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o plugin.pico plugin.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kfunc.o test/test_kfunc.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kstring.o test/test_kstring.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_str2int.o test/test_str2int.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_index.o test/test_index.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-parse-reg.o test/test-parse-reg.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 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c gcc -shared -Wl,-soname,libhts.so.3 -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/string_alloc.pico plugin.pico -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/hts_endian test/hts_endian.o -ldeflate -llzma -lbz2 -lz -lm -ldl gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -llzma -lbz2 -lz -lm -ldl ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o plugin.o ranlib libhts.a gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread ln -sf libhts.so libhts.so.3 gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/sam test/sam.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_kfunc test/test_kfunc.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -llzma -lbz2 -lz -lm -ldl -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -llzma -lbz2 -lz -lm -ldl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -llzma -lbz2 -lz -lm -ldl -lcrypto -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden -o hfile_s3_write.so hfile_s3_write.pico libhts.so -ldeflate -llzma -lbz2 -lz -lm -ldl -lcrypto -lcurl -lpthread make[2]: Leaving directory '/build/reproducible-path/htslib-1.11' make[1]: Leaving directory '/build/reproducible-path/htslib-1.11' rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/htslib-1.11' dh_auto_test -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \ PACKAGE_VERSION="1.11-4" \ 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 -j3 test VERBOSE=1 "CFLAGS=-g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden" PACKAGE_VERSION=1.11-4 libdir=/usr/lib/arm-linux-gnueabihf make[2]: Entering directory '/build/reproducible-path/htslib-1.11' test/hts_endian test/test_kfunc test/test_kstring test/test_str2int test/fieldarith test/fieldarith.sam test/hfile HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" Expected error: [E::hts_parse_region] Unexpected string "x" after region Expected error: [E::hts_parse_region] Unexpected string "y" after region Expected error: [E::hts_parse_region] Unexpected string "chr3" after region cd test/tabix && ./test-tabix.sh tabix.tst Testing tabix... PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 Expected passes: 14 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/mpileup && ./test-pileup.sh mpileup.tst Testing (m)pileup... PASS : $pileup mp_D.sam PASS : $pileup -m mp_D.sam PASS : $pileup mp_DI.sam PASS : $pileup -m mp_DI.sam PASS : $pileup mp_I.sam PASS : $pileup -m mp_I.sam PASS : $pileup mp_P.sam PASS : $pileup -m mp_P.sam PASS : $pileup mp_ID.sam PASS : $pileup -m mp_ID.sam PASS : $pileup mp_N.sam PASS : $pileup -m mp_N.sam PASS : $pileup mp_N2.sam PASS : $pileup -m mp_N2.sam PASS : $pileup c1#pad1.sam PASS : $pileup -m c1#pad1.sam PASS : $pileup c1#pad2.sam PASS : $pileup -m c1#pad2.sam PASS : $pileup c1#pad3.sam PASS : $pileup -m c1#pad3.sam PASS : $pileup -m small.bam Expected passes: 21 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx.fa test/fastqs.fq test/test-regidx cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} bgzip round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -l 0 -b -m 14 -x /tmp/TedoC24iA4/index.bam.csi /build/reproducible-path/htslib-1.11/test/index.sam > /tmp/TedoC24iA4/index.bam .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -c /tmp/TedoC24iA4/index.bam .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -l 0 -b -m 0 -x /tmp/TedoC24iA4/index.bam.bai /build/reproducible-path/htslib-1.11/test/index.sam > /tmp/TedoC24iA4/index.bam .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -b /tmp/TedoC24iA4/index.bam .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -l 0 -z -m 14 -x /tmp/TedoC24iA4/index.sam.gz.csi /build/reproducible-path/htslib-1.11/test/index.sam > /tmp/TedoC24iA4/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -c /tmp/TedoC24iA4/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -l 0 -z -m 0 -x /tmp/TedoC24iA4/index.sam.gz.bai /build/reproducible-path/htslib-1.11/test/index.sam > /tmp/TedoC24iA4/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -b /tmp/TedoC24iA4/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -l 0 -C -x /tmp/TedoC24iA4/index.cram.crai /build/reproducible-path/htslib-1.11/test/index.sam > /tmp/TedoC24iA4/index.cram .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index /tmp/TedoC24iA4/index.cram .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -l 0 -b -m 14 -x /tmp/TedoC24iA4/index.bcf.csi /build/reproducible-path/htslib-1.11/test/index.vcf > /tmp/TedoC24iA4/index.bcf .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -c /tmp/TedoC24iA4/index.bcf .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -l 0 -z -m 14 -x /tmp/TedoC24iA4/index.vcf.gz.csi /build/reproducible-path/htslib-1.11/test/index.vcf > /tmp/TedoC24iA4/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -c /tmp/TedoC24iA4/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -l 0 -z -m 0 -x /tmp/TedoC24iA4/index.vcf.gz.tbi /build/reproducible-path/htslib-1.11/test/index.vcf > /tmp/TedoC24iA4/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -t /tmp/TedoC24iA4/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.11/tabix /tmp/TedoC24iA4/index.vcf.gz##idx##/tmp/TedoC24iA4/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -@4 -l 0 -b -m 14 -x /tmp/TedoC24iA4/index.bam.csi /build/reproducible-path/htslib-1.11/test/index.sam > /tmp/TedoC24iA4/index.bam .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -c /tmp/TedoC24iA4/index.bam .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -@4 -l 0 -b -m 0 -x /tmp/TedoC24iA4/index.bam.bai /build/reproducible-path/htslib-1.11/test/index.sam > /tmp/TedoC24iA4/index.bam .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -b /tmp/TedoC24iA4/index.bam .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -@4 -l 0 -z -m 14 -x /tmp/TedoC24iA4/index.sam.gz.csi /build/reproducible-path/htslib-1.11/test/index.sam > /tmp/TedoC24iA4/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -c /tmp/TedoC24iA4/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -@4 -l 0 -z -m 0 -x /tmp/TedoC24iA4/index.sam.gz.bai /build/reproducible-path/htslib-1.11/test/index.sam > /tmp/TedoC24iA4/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -b /tmp/TedoC24iA4/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -@4 -l 0 -C -x /tmp/TedoC24iA4/index.cram.crai /build/reproducible-path/htslib-1.11/test/index.sam > /tmp/TedoC24iA4/index.cram .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index /tmp/TedoC24iA4/index.cram .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -@4 -l 0 -b -m 14 -x /tmp/TedoC24iA4/index.bcf.csi /build/reproducible-path/htslib-1.11/test/index.vcf > /tmp/TedoC24iA4/index.bcf .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -c /tmp/TedoC24iA4/index.bcf .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -@4 -l 0 -z -m 14 -x /tmp/TedoC24iA4/index.vcf.gz.csi /build/reproducible-path/htslib-1.11/test/index.vcf > /tmp/TedoC24iA4/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -c /tmp/TedoC24iA4/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_view -@4 -l 0 -z -m 0 -x /tmp/TedoC24iA4/index.vcf.gz.tbi /build/reproducible-path/htslib-1.11/test/index.vcf > /tmp/TedoC24iA4/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.11/test/test_index -t /tmp/TedoC24iA4/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.11/tabix /tmp/TedoC24iA4/index.vcf.gz##idx##/tmp/TedoC24iA4/index.vcf.gz.tbi 1:10000060-10000060 .. 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 -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 -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=2.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -t auxf.fa -S -l0 -C -o VERSION=3.0 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 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram ./test_view -t auxf.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram ./test_view auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.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 -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 -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=2.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram ./test_view c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -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 -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=2.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram ./test_view c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -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 -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=2.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram ./test_view c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -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 -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=2.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram ./test_view c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -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 -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=2.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram ./test_view c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -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 -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=2.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram ./test_view 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 -S -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 -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=2.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram ./test_view c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -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 -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=2.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -t c2.fa -S -l0 -C -o VERSION=3.0 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 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram ./test_view -t c2.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram ./test_view c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -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 -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=2.1 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram ./test_view ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.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 -C -o VERSION=2.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam ./test_view ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.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 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam ./test_view ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.cram > ce#1000.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram ./test_view ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -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 -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=2.1 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram ./test_view ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -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 -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=2.1 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram ./test_view 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 -S -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 -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=2.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram ./test_view ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.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 -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 -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=2.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view ce#large_seq.tmp.bam.cram.bam > 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 -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view ce#large_seq.tmp.bam.cram.bam > 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 -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram ./test_view 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 -S -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 -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=2.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram ./test_view 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 -S -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 -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=2.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram ./test_view 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_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -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 -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=2.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram ./test_view 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_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -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 -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=2.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram ./test_view ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -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 -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=2.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram ./test_view ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -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 -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=2.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram ./test_view ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -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 -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=2.1 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam ./test_view md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -t md.fa -S -l0 -C -o VERSION=3.0 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 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam ./test_view md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -t md.fa -C -o VERSION=2.1 md#1.tmp.cram > md#1.tmp.cram.cram ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.cram.cram > md#1.tmp.cram ./test_view -t md.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram ./test_view md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -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 -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=2.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram ./test_view 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 -S -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 -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=2.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view xx#large_aux.tmp.bam.cram.bam > 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 -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view xx#large_aux.tmp.bam.cram.bam > 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 -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram ./test_view 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 -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 -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 -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=2.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram ./test_view 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_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -S -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 -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=2.1 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam ./test_view xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam ./test_view xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#MD.tmp.cram > xx#MD.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram.cram > xx#MD.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram ./test_view 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 -S -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 -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=2.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam ./test_view xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam ./test_view xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram ./test_view xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -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 -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=2.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram ./test_view xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -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 -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=2.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram ./test_view 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 -S -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 -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=2.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram ./test_view xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -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 -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=2.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram ./test_view xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -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 -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=2.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram ./test_view 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 -S -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 -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=2.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram ./test_view xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -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 -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=2.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram ./test_view xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -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 -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=2.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram ./test_view xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.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 .. 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-1.11/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 -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 -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=2.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view -@4 auxf#values.tmp.bam.cram.bam > 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 -l0 -C -o VERSION=3.0 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 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view -@4 auxf#values.tmp.bam.cram.bam > 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 -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram ./test_view -@4 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 -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 -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=2.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view -@4 c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view -@4 c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram ./test_view -@4 c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -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 -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=2.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view -@4 c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view -@4 c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram ./test_view -@4 c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -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 -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=2.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view -@4 c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view -@4 c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram ./test_view -@4 c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -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 -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=2.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view -@4 c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view -@4 c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram ./test_view -@4 c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -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 -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=2.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view -@4 c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view -@4 c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram ./test_view -@4 c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -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 -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=2.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view -@4 c1#pad3.tmp.bam.cram.bam > 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 -l0 -C -o VERSION=3.0 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 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view -@4 c1#pad3.tmp.bam.cram.bam > 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 -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram ./test_view -@4 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 -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 -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=2.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view -@4 c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 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 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view -@4 c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram ./test_view -@4 c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -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 -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=2.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view -@4 c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c2.fa -S -l0 -C -o VERSION=3.0 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 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view -@4 c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram ./test_view -@4 -t c2.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram ./test_view -@4 c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -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 -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=2.1 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view -@4 ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view -@4 ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram ./test_view -@4 ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.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 -C -o VERSION=2.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam ./test_view -@4 ce#1000.tmp.bam.cram.bam > 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 -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 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam ./test_view -@4 ce#1000.tmp.bam.cram.bam > 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=2.1 ce#1000.tmp.cram > ce#1000.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram ./test_view -@4 ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -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 -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=2.1 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view -@4 ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view -@4 ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram ./test_view -@4 ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -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 -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=2.1 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view -@4 ce#5.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view -@4 ce#5.tmp.bam.cram.bam > 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=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram ./test_view -@4 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 -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 -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=2.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view -@4 ce#5b.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view -@4 ce#5b.tmp.bam.cram.bam > 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=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram ./test_view -@4 ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.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 -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 -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=2.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view -@4 ce#large_seq.tmp.bam.cram.bam > 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 -l0 -C -o VERSION=3.0 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 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view -@4 ce#large_seq.tmp.bam.cram.bam > 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 -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram ./test_view -@4 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 -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 -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=2.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view -@4 ce#supp.tmp.bam.cram.bam > 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 -l0 -C -o VERSION=3.0 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 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view -@4 ce#supp.tmp.bam.cram.bam > 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 -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram ./test_view -@4 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 -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 -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=2.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view -@4 ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view -@4 ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram ./test_view -@4 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_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -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 -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=2.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view -@4 ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 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 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view -@4 ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram ./test_view -@4 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_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -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 -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=2.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view -@4 ce#unmap.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view -@4 ce#unmap.tmp.bam.cram.bam > 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=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram ./test_view -@4 ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -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 -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=2.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view -@4 ce#unmap1.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view -@4 ce#unmap1.tmp.bam.cram.bam > 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=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram ./test_view -@4 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -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 -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=2.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view -@4 ce#unmap2.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view -@4 ce#unmap2.tmp.bam.cram.bam > 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=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram ./test_view -@4 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -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 -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=2.1 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam ./test_view -@4 md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t md.fa -S -l0 -C -o VERSION=3.0 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 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam ./test_view -@4 md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t md.fa -C -o VERSION=2.1 md#1.tmp.cram > md#1.tmp.cram.cram ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.cram.cram > md#1.tmp.cram ./test_view -@4 -t md.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram ./test_view -@4 md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -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 -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=2.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view -@4 xx#blank.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view -@4 xx#blank.tmp.bam.cram.bam > 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=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram ./test_view -@4 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 -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 -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=2.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view -@4 xx#large_aux.tmp.bam.cram.bam > 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 -l0 -C -o VERSION=3.0 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 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view -@4 xx#large_aux.tmp.bam.cram.bam > 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 -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram ./test_view -@4 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 -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 -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=2.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view -@4 xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view -@4 xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram ./test_view -@4 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_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -@4 -S -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 -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=2.1 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam ./test_view -@4 xx#MD.tmp.bam.cram.bam > 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 -l0 -C -o VERSION=3.0 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 -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam ./test_view -@4 xx#MD.tmp.bam.cram.bam > 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 -C -o VERSION=2.1 xx#MD.tmp.cram > xx#MD.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram.cram > xx#MD.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram ./test_view -@4 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 -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 -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=2.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam ./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam ./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram ./test_view -@4 xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -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 -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=2.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view -@4 xx#minimal.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view -@4 xx#minimal.tmp.bam.cram.bam > 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=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram ./test_view -@4 xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -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 -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=2.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view -@4 xx#pair.tmp.bam.cram.bam > 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 -l0 -C -o VERSION=3.0 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 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view -@4 xx#pair.tmp.bam.cram.bam > 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 -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram ./test_view -@4 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 -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 -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=2.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view -@4 xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view -@4 xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram ./test_view -@4 xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -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 -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=2.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view -@4 xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view -@4 xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram ./test_view -@4 xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -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 -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=2.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view -@4 xx#tlen.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view -@4 xx#tlen.tmp.bam.cram.bam > 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=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram ./test_view -@4 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 -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 -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=2.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view -@4 xx#tlen2.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view -@4 xx#tlen2.tmp.bam.cram.bam > 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=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram ./test_view -@4 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -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 -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=2.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view -@4 xx#triplet.tmp.bam.cram.bam > 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 -S -l0 -C -o VERSION=3.0 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 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view -@4 xx#triplet.tmp.bam.cram.bam > 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=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram ./test_view -@4 xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -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 -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=2.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view -@4 xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 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 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view -@4 xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram ./test_view -@4 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.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 .. 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-1.11/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-1.11/test/test-vcf-api /tmp/TedoC24iA4/test-vcf-api.bcf [E::bcf_index_build3] TBI indices for BCF files are not supported [E::idx_find_and_load] Could not retrieve index file for '/tmp/TedoC24iA4/test-vcf-api.bcf' .. ok test_bcf2vcf: /build/reproducible-path/htslib-1.11/test/test_view /build/reproducible-path/htslib-1.11/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /build/reproducible-path/htslib-1.11/test/test-vcf-sweep /tmp/TedoC24iA4/test-vcf-api.bcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.11/htsfile -ch /build/reproducible-path/htslib-1.11/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.11/htsfile -c /build/reproducible-path/htslib-1.11/test/formatcols.vcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.11/htsfile -c /build/reproducible-path/htslib-1.11/test/noroundtrip.vcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.11/htsfile -c /build/reproducible-path/htslib-1.11/test/formatmissing.vcf .. ok test-bcf-sr: /build/reproducible-path/htslib-1.11/test/test-bcf-sr.pl -t /tmp/TedoC24iA4 -s 935205174 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.11/test/test-bcf-sr.pl -t /tmp/TedoC24iA4 -s 322182142 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.11/test/test-bcf-sr.pl -t /tmp/TedoC24iA4 -s 1024892529 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.11/test/test-bcf-sr.pl -t /tmp/TedoC24iA4 -s 567231539 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.11/test/test-bcf-sr.pl -t /tmp/TedoC24iA4 -s 1128169198 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.11/test/test-bcf-sr.pl -t /tmp/TedoC24iA4 -s 645901640 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.11/test/test-bcf-sr.pl -t /tmp/TedoC24iA4 -s 1041447829 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.11/test/test-bcf-sr.pl -t /tmp/TedoC24iA4 -s 286585957 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.11/test/test-bcf-sr.pl -t /tmp/TedoC24iA4 -s 1095536008 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.11/test/test-bcf-sr.pl -t /tmp/TedoC24iA4 -s 1618079773 .. ok test_command: /build/reproducible-path/htslib-1.11/test/test-bcf-translate - .. ok test_convert_padded_header: /build/reproducible-path/htslib-1.11/test/test_view -t ce.fa -C /tmp/TedoC24iA4/headernul0.bam .. ok test_convert_padded_header: /build/reproducible-path/htslib-1.11/test/test_view -t ce.fa -C /tmp/TedoC24iA4/headernul1.bam .. ok test_convert_padded_header: /build/reproducible-path/htslib-1.11/test/test_view -t ce.fa -C /tmp/TedoC24iA4/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /build/reproducible-path/htslib-1.11/bgzip -I /build/reproducible-path/htslib-1.11/test/bgziptest.txt.tmp.gz.gzi -c -g /build/reproducible-path/htslib-1.11/test/bgziptest.txt .. ok test-logging: /build/reproducible-path/htslib-1.11/test/test-logging.pl .. ok test_realn: /build/reproducible-path/htslib-1.11/test/test_realn -f /build/reproducible-path/htslib-1.11/test/realn01.fa -i /build/reproducible-path/htslib-1.11/test/realn01.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.11/test/test_realn -f /build/reproducible-path/htslib-1.11/test/realn02.fa -i /build/reproducible-path/htslib-1.11/test/realn02.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.11/test/test_realn -a -f /build/reproducible-path/htslib-1.11/test/realn01.fa -i /build/reproducible-path/htslib-1.11/test/realn01.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.11/test/test_realn -a -f /build/reproducible-path/htslib-1.11/test/realn02.fa -i /build/reproducible-path/htslib-1.11/test/realn02.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.11/test/test_realn -e -f /build/reproducible-path/htslib-1.11/test/realn01.fa -i /build/reproducible-path/htslib-1.11/test/realn01.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.11/test/test_realn -e -f /build/reproducible-path/htslib-1.11/test/realn02.fa -i /build/reproducible-path/htslib-1.11/test/realn02.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.11/test/test_realn -r -f /build/reproducible-path/htslib-1.11/test/realn02.fa -i /build/reproducible-path/htslib-1.11/test/realn02-r.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.11/test/test_realn -a -f /build/reproducible-path/htslib-1.11/test/realn02.fa -i /build/reproducible-path/htslib-1.11/test/realn02_exp.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.11/test/test_realn -f /build/reproducible-path/htslib-1.11/test/realn02.fa -i /build/reproducible-path/htslib-1.11/test/realn02_exp-a.sam -o - .. ok Number of tests: total .. 154 passed .. 154 failed .. 0 make[2]: Leaving directory '/build/reproducible-path/htslib-1.11' rm -fr -- /tmp/dh-xdg-rundir-_yVeuQCP make[1]: Leaving directory '/build/reproducible-path/htslib-1.11' rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/reproducible-path/htslib-1.11' echo "Suppress test for Architecture independant builds." Suppress test for Architecture independant builds. make[1]: Leaving directory '/build/reproducible-path/htslib-1.11' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/libhts3.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars rm -fr -- debian/.debhelper/generated/libhts3/ debian/libhts3/ 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-1.11' for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \ rm /build/reproducible-path/htslib-1.11/test/${binary} ; \ done dh_auto_install -- prefix=/usr \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \ PACKAGE_VERSION="1.11-4" \ libdir=/usr/lib/arm-linux-gnueabihf install -d /build/reproducible-path/htslib-1.11/debian/tmp make -j3 install DESTDIR=/build/reproducible-path/htslib-1.11/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr "CFLAGS=-g -O2 -fdebug-prefix-map=/build/reproducible-path/htslib-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -flto -fvisibility=hidden" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -Wl,-flto -fvisibility=hidden" PACKAGE_VERSION=1.11-4 libdir=/usr/lib/arm-linux-gnueabihf make[2]: Entering directory '/build/reproducible-path/htslib-1.11' mkdir -p -m 755 /build/reproducible-path/htslib-1.11/debian/tmp/usr/bin /build/reproducible-path/htslib-1.11/debian/tmp/usr/include /build/reproducible-path/htslib-1.11/debian/tmp/usr/include/htslib /build/reproducible-path/htslib-1.11/debian/tmp/usr/lib/arm-linux-gnueabihf /build/reproducible-path/htslib-1.11/debian/tmp/usr/share/man/man1 /build/reproducible-path/htslib-1.11/debian/tmp/usr/share/man/man5 /build/reproducible-path/htslib-1.11/debian/tmp/usr/share/man/man7 /build/reproducible-path/htslib-1.11/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig if test -n "/htslib"; then mkdir -p -m 755 /build/reproducible-path/htslib-1.11/debian/tmp/htslib; fi install -p -m 644 libhts.so /build/reproducible-path/htslib-1.11/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.11-4 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/arm-linux-gnueabihf#g;s#@-PACKAGE_VERSION@#1.11-4#g' htslib.pc.tmp > /build/reproducible-path/htslib-1.11/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc chmod 644 /build/reproducible-path/htslib-1.11/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc ln -sf libhts.so.1.11-4 /build/reproducible-path/htslib-1.11/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so ln -sf libhts.so.1.11-4 /build/reproducible-path/htslib-1.11/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3 install -p bgzip htsfile tabix /build/reproducible-path/htslib-1.11/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-1.11/debian/tmp/htslib; fi install -p -m 644 htslib/*.h /build/reproducible-path/htslib-1.11/debian/tmp/usr/include/htslib install -p -m 644 libhts.a /build/reproducible-path/htslib-1.11/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a install -p -m 644 bgzip.1 htsfile.1 tabix.1 /build/reproducible-path/htslib-1.11/debian/tmp/usr/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /build/reproducible-path/htslib-1.11/debian/tmp/usr/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /build/reproducible-path/htslib-1.11/debian/tmp/usr/share/man/man7 make[2]: Leaving directory '/build/reproducible-path/htslib-1.11' # 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-1.11' rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/htslib-1.11' dh_install --indep install -d debian/.debhelper/generated/libhts3 install -d debian/.debhelper/generated/libhts-dev install -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 -d debian/htslib-test/usr/share/htslib-test cp --reflink=auto -a ./Makefile ./bcf_sr_sort.c ./bcf_sr_sort.h ./bgzf.c ./bgzip.c ./config.h ./config.mk ./errmod.c ./faidx.c ./header.c ./header.h ./hfile.c ./hfile_gcs.c ./hfile_internal.h ./hfile_libcurl.c ./hfile_net.c ./hfile_s3.c ./hfile_s3_write.c ./hts.c ./hts_internal.h ./hts_os.c ./htsfile.c ./htslib.mk ./htslib_static.mk ./htslib_vars.mk ./kfunc.c ./knetfile.c ./kstring.c ./md5.c ./multipart.c ./os ./plugin.c ./probaln.c ./realn.c ./regidx.c ./region.c ./sam.c ./sam_internal.h ./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 -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.c ./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/rANS_byte.h ./cram/rANS_static.c ./cram/rANS_static.h ./cram/string_alloc.c ./cram/string_alloc.h debian/htslib-test/usr/share/htslib-test/cram/ install -d debian/htslib-test/usr/share/htslib-test/test cp --reflink=auto -a ./test/auxf\#values.sam ./test/auxf\#values_java.cram ./test/auxf.fa ./test/auxf.fa.fai ./test/bcf-sr ./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.fa ./test/fastqs.fq ./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/longrefs ./test/maintainer ./test/md\#1.sam ./test/md.fa ./test/md.fa.fai ./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/plugins-dlhts.c ./test/range.bam ./test/range.bam.bai ./test/range.cram ./test/range.cram.crai ./test/range.out ./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/sam.c ./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-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_index.c ./test/test_kfunc.c ./test/test_kstring.c ./test/test_realn.c ./test/test_str2int.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/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/ install -d debian/.debhelper/generated/htslib-test install -d debian/.debhelper/generated/tabix 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-1.11' dh_install -Nhtslib-test install -d debian/libhts3/usr/lib/arm-linux-gnueabihf cp --reflink=auto -a ./debian/tmp/htslib debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.11-4 debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3 debian/libhts3/usr/lib/arm-linux-gnueabihf/ install -d debian/libhts3/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/libhts3/usr/share/man/man5/ install -d debian/libhts-dev/usr/include cp --reflink=auto -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/ install -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 -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 -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-1.11' dh_installdocs install -d debian/libhts3/usr/share/doc/libhts3 install -p -m0644 debian/copyright debian/libhts3/usr/share/doc/libhts3/copyright install -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 -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/copyright debian/htslib-test/usr/share/doc/htslib-test/copyright install -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-1.11' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/htslib-1.11' dh_installchangelogs NEWS install -p -m0644 debian/changelog debian/libhts3/usr/share/doc/libhts3/changelog.Debian install -p -m0644 NEWS debian/libhts3/usr/share/doc/libhts3/changelog install -p -m0644 debian/changelog debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog install -p -m0644 debian/changelog debian/htslib-test/usr/share/doc/htslib-test/changelog.Debian install -p -m0644 NEWS debian/htslib-test/usr/share/doc/htslib-test/changelog install -p -m0644 debian/changelog debian/tabix/usr/share/doc/tabix/changelog.Debian install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog make[1]: Leaving directory '/build/reproducible-path/htslib-1.11' dh_installman install -d debian/libhts3/usr/share/man/man7/ install -p -m0644 ./htslib-s3-plugin.7 debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7 install -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./htsfile.1 debian/tabix/usr/share/man/man1/htsfile.1 install -p -m0644 ./tabix.1 debian/tabix/usr/share/man/man1/tabix.1 install -p -m0644 ./bgzip.1 debian/tabix/usr/share/man/man1/bgzip.1 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man5/faidx.5 debian/libhts3/usr/share/man/man5/sam.5 debian/libhts3/usr/share/man/man5/vcf.5 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7 debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/tabix.1 mv debian/libhts3/usr/share/man/man5/faidx.5.dh-new debian/libhts3/usr/share/man/man5/faidx.5 mv debian/libhts3/usr/share/man/man5/sam.5.dh-new debian/libhts3/usr/share/man/man5/sam.5 mv debian/libhts3/usr/share/man/man5/vcf.5.dh-new debian/libhts3/usr/share/man/man5/vcf.5 chmod 0644 -- debian/libhts3/usr/share/man/man5/faidx.5 debian/libhts3/usr/share/man/man5/sam.5 debian/libhts3/usr/share/man/man5/vcf.5 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/libhts3/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3/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/libhts3/usr/share/man/man7/htslib-s3-plugin.7 debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1 dh_lintian install -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 (grep -a -s -v perl:Depends debian/htslib-test.substvars; echo perl:Depends=perl:any) > debian/htslib-test.substvars.new mv debian/htslib-test.substvars.new debian/htslib-test.substvars dh_link rm -f debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.3 ln -s libhts.so.1.11-4 debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.3 rm -f debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so ln -s libhts.so.1.11-4 debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so 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/libhts3 cd debian/htslib-test chmod a-x usr/share/doc/libhts3/changelog usr/share/doc/libhts3/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/libhts3/changelog usr/share/doc/libhts3/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 cd '/build/reproducible-path/htslib-1.11' chmod a-x usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian cd debian/libhts-dev 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/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian cd '/build/reproducible-path/htslib-1.11' cd debian/tabix cd '/build/reproducible-path/htslib-1.11' 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/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 cd '/build/reproducible-path/htslib-1.11' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/htslib-1.11' dh_fixperms find debian/libhts3 ! -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/libhts3/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts3/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3/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 f -a -true -a ! -regex 'debian/htslib-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts3/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3 -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/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/libhts3/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/tabix ! -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 ! -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 d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tabix/usr/share/man -type f -a -true -a -true -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/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/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/libhts-dev/usr/include -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/libhts-dev/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-1.11' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/htslib-1.11' # 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-1.11' dh_dwz -a install -d debian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf dwz -mdebian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug -- debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.11-4 dwz: debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.11-4: DWARF compression not beneficial - old size 747810 new size 756326 objcopy --compress-debug-sections debian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug install -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 objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_strip make[1]: Entering directory '/build/reproducible-path/htslib-1.11' # This is apparently important for the interpretation by ldc2 in sambamba dh_strip -Xlibhts.a install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/bb objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.11-4 debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/bb/11a972bccebb3e6ad62f2066a27854c4751f5e.debug install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e0 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e0/a44f30c6daf5d9a93cd3f396334fdafabd208d.debug chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/bb/11a972bccebb3e6ad62f2066a27854c4751f5e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.11-4 objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/bb/11a972bccebb3e6ad62f2066a27854c4751f5e.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.11-4 install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/48 objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/48/ea7dcf861e6c143b4d181ef7b53c1b84aad8e4.debug chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/48/ea7dcf861e6c143b4d181ef7b53c1b84aad8e4.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e0/a44f30c6daf5d9a93cd3f396334fdafabd208d.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/tabix objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/48/ea7dcf861e6c143b4d181ef7b53c1b84aad8e4.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/0b objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/0b/617923f35f7372d367fd0b382212034817f085.debug objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e0/a44f30c6daf5d9a93cd3f396334fdafabd208d.debug debian/tabix/usr/bin/tabix chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/0b/617923f35f7372d367fd0b382212034817f085.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/0b/617923f35f7372d367fd0b382212034817f085.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/01 objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/01/59710d646b61a4adfeff92ebd3d1427c630788.debug chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/01/59710d646b61a4adfeff92ebd3d1427c630788.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/01/59710d646b61a4adfeff92ebd3d1427c630788.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/72 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/72/3c4a802f1fafc15b8116f01ff64267548e8a9f.debug install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/61 objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/61/bd03ecd7e554c5546db3cdc571843f71896569.debug chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/61/bd03ecd7e554c5546db3cdc571843f71896569.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/61/bd03ecd7e554c5546db3cdc571843f71896569.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/libhts3/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/libhts3/usr/lib/debug install -d debian/.debhelper/libhts3/dbgsym-root/usr/share/doc ln -s libhts3 debian/.debhelper/libhts3/dbgsym-root/usr/share/doc/libhts3-dbgsym chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/72/3c4a802f1fafc15b8116f01ff64267548e8a9f.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/72/3c4a802f1fafc15b8116f01ff64267548e8a9f.debug debian/tabix/usr/bin/bgzip install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e6 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e6/df64bc4f4782ee4a92b4a2142d9f234d5ce186.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e6/df64bc4f4782ee4a92b4a2142d9f234d5ce186.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/e6/df64bc4f4782ee4a92b4a2142d9f234d5ce186.debug debian/tabix/usr/bin/htsfile install -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 -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym make[1]: Leaving directory '/build/reproducible-path/htslib-1.11' dh_makeshlibs -a rm -f debian/libhts3/DEBIAN/shlibs install -d debian/libhts3/DEBIAN echo "libhts 3 libhts3 (>= 1.11)" >> debian/libhts3/DEBIAN/shlibs chmod 0644 -- debian/libhts3/DEBIAN/shlibs dpkg-gensymbols -plibhts3 -Idebian/libhts3.symbols -Pdebian/libhts3 -edebian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.11-4 mv debian/.debhelper/generated/libhts3/triggers.new debian/.debhelper/generated/libhts3/triggers rm -f debian/libhts-dev/DEBIAN/shlibs rm -f debian/tabix/DEBIAN/shlibs dh_shlibdeps -a install -d debian/tabix/DEBIAN dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/tabix debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile dpkg-shlibdeps -Tdebian/libhts3.substvars debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.11-4 debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so dh_installdeb install -p -m0644 debian/.debhelper/generated/libhts3/triggers debian/libhts3/DEBIAN/triggers install -d debian/libhts-dev/DEBIAN install -d debian/htslib-test/DEBIAN dh_gencontrol 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 -Pdebian/htslib-test echo misc:Depends= >> debian/libhts3.substvars echo misc:Pre-Depends= >> debian/libhts3.substvars install -d debian/.debhelper/libhts3/dbgsym-root/DEBIAN dpkg-gencontrol -plibhts3 -ldebian/changelog -Tdebian/libhts3.substvars -Pdebian/.debhelper/libhts3/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=libhts3-dbgsym "-DDepends=libhts3 (= \${binary:Version})" "-DDescription=debug symbols for libhts3" "-DBuild-Ids=0159710d646b61a4adfeff92ebd3d1427c630788 0b617923f35f7372d367fd0b382212034817f085 48ea7dcf861e6c143b4d181ef7b53c1b84aad8e4 61bd03ecd7e554c5546db3cdc571843f71896569 bb11a972bccebb3e6ad62f2066a27854c4751f5e" -DSection=debug -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibhts3 -ldebian/changelog -Tdebian/libhts3.substvars -Pdebian/libhts3 chmod 0644 -- debian/htslib-test/DEBIAN/control echo misc:Depends= >> debian/tabix.substvars echo misc:Pre-Depends= >> debian/tabix.substvars install -d debian/.debhelper/tabix/dbgsym-root/DEBIAN dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/.debhelper/tabix/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=723c4a802f1fafc15b8116f01ff64267548e8a9f e0a44f30c6daf5d9a93cd3f396334fdafabd208d e6df64bc4f4782ee4a92b4a2142d9f234d5ce186" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/libhts3/DEBIAN/control 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 -Pdebian/libhts-dev chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix chmod 0644 -- debian/tabix/DEBIAN/control chmod 0644 -- debian/libhts-dev/DEBIAN/control dh_md5sums cd debian/htslib-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libhts3 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts3/DEBIAN/md5sums chmod 0644 -- debian/htslib-test/DEBIAN/md5sums cd debian/.debhelper/libhts3/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/tabix/DEBIAN/md5sums cd debian/libhts-dev >/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/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/tabix .. dpkg-deb --root-owner-group --build debian/libhts3 .. dpkg-deb: building package 'libhts3' in '../libhts3_1.11-4_armhf.deb'. dpkg-deb --root-owner-group --build debian/libhts-dev .. dpkg-deb: building package 'tabix' in '../tabix_1.11-4_armhf.deb'. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.11-4_armhf.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root .. dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.11-4_armhf.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/libhts3/dbgsym-root .. dpkg-deb: building package 'libhts3-dbgsym' in '../libhts3-dbgsym_1.11-4_armhf.deb'. dpkg-deb --root-owner-group --build debian/htslib-test .. dpkg-deb: building package 'htslib-test' in '../htslib-test_1.11-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../htslib_1.11-4_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from htslib-1.11/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: 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/15890 and its subdirectories I: Current time: Mon Jan 8 08:23:23 -12 2024 I: pbuilder-time-stamp: 1704745403 Mon Jan 8 20:23:43 UTC 2024 I: 1st build successful. Starting 2nd build on remote node cbxi4b-armhf-rb.debian.net. Mon Jan 8 20:23:43 UTC 2024 I: Preparing to do remote build '2' on cbxi4b-armhf-rb.debian.net. Mon Jan 8 21:23:40 UTC 2024 I: Deleting $TMPDIR on cbxi4b-armhf-rb.debian.net. Mon Jan 8 21:23:43 UTC 2024 I: htslib_1.11-4_armhf.changes: Format: 1.8 Date: Sat, 02 Jan 2021 16:28:22 +0100 Source: htslib Binary: htslib-test libhts-dev libhts3 libhts3-dbgsym tabix tabix-dbgsym Architecture: all armhf Version: 1.11-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: htslib-test - Test data for HTSlib libhts-dev - development files for the HTSlib libhts3 - C library for high-throughput sequencing data formats tabix - generic indexer for TAB-delimited genome position files Closes: 978094 Changes: htslib (1.11-4) unstable; urgency=medium . * libhts3: Breaks+Replaces: libhts-dev (<< 1.11-3). Closes: #978094 Checksums-Sha1: d22b7a101ef612ad7a3aae275233a1bb4b6b7f1f 1034204 htslib-test_1.11-4_all.deb 29b1cfc6bca84ceffe9a891b53a0f8cfa49a4cc3 6936 htslib_1.11-4_armhf.buildinfo c1ffe5e23b2e897cfaf5753b39b4fc9a6af6fdd9 3836604 libhts-dev_1.11-4_armhf.deb 34d813baca9624d0d37c7c98675139030a0b6872 1075648 libhts3-dbgsym_1.11-4_armhf.deb 1a983390c3f678efdc8b744398fcf0c9d6698df7 332540 libhts3_1.11-4_armhf.deb 5ada1066462e490ec3a2e6995e349633a6874fb4 1392512 tabix-dbgsym_1.11-4_armhf.deb 9829c0a3103e09bfa0f38e8c01d87871ab95ea71 305912 tabix_1.11-4_armhf.deb Checksums-Sha256: 7e2430f38502247a955d5ddc11aa5869881bf28a039642dd69de3e81ce500ac4 1034204 htslib-test_1.11-4_all.deb 31af2603783591ac7f98258107cb1f9cfc9fe73ddbbb2894840f604e73d54aed 6936 htslib_1.11-4_armhf.buildinfo 23aa74dd8319336dce341214c652db1af7c0fe5e06d47e807e9a298f71d66f7e 3836604 libhts-dev_1.11-4_armhf.deb 0a6a6f7c658a11809b05ab1576aeb731ed90deafe8a4d57479ea79f9cc4c1274 1075648 libhts3-dbgsym_1.11-4_armhf.deb d6d1520d52c236c8eea926211afd64c00f6fa824d471ab1cffcf2c85a0d27cfa 332540 libhts3_1.11-4_armhf.deb 21d04495dc6ae8a323e8c764f5e8cb7318161b838b64a2c9712b9ebfffa2cc8f 1392512 tabix-dbgsym_1.11-4_armhf.deb 22e9e93b7c61948fcc1224a74e40f6cfc00158a9edd18c6b127caeced9eea1d8 305912 tabix_1.11-4_armhf.deb Files: 586cd54a305f61d80a36091218dfb9f8 1034204 science optional htslib-test_1.11-4_all.deb c29b5f0ffc5e6315498e23a72b02e1ca 6936 science optional htslib_1.11-4_armhf.buildinfo cf3b9ce044bcbccb7d9ab9fb9ff7aa33 3836604 libdevel optional libhts-dev_1.11-4_armhf.deb d7289fbb483dbbfac7edf8f519121e8c 1075648 debug optional libhts3-dbgsym_1.11-4_armhf.deb c8ed2d16d7f36331a1eda6393dd8b1d8 332540 libs optional libhts3_1.11-4_armhf.deb 2e898888335561d8d01489c9fb56c526 1392512 debug optional tabix-dbgsym_1.11-4_armhf.deb f1e9052bdcd5713a543b418758dadfd9 305912 science optional tabix_1.11-4_armhf.deb Mon Jan 8 21:23:44 UTC 2024 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.gzc3bV7t/htslib_1.11-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.gzc3bV7t/htslib_1.11-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.gzc3bV7t/htslib_1.11-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.gzc3bV7t/b1/htslib_1.11-4_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.gzc3bV7t/b2/htslib_1.11-4_armhf.changes ## close_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.ar.ArContainer ## command (total time: 11.900s) 6.517s 1528 calls diff 3.968s 15491 calls readelf 0.612s 440 calls strings 0.524s 6 calls xz 0.119s 11 calls nm 0.059s 880 calls objdump 0.047s 20 calls cmp 0.047s 20 calls cmp (external) 0.004s 50 calls cmp (internal) 0.003s 80 calls objcopy ## compare_files (cumulative) (total time: 127.388s) 20.333s 1 call abc.DotChangesFile 20.275s 1 call abc.DebFile 20.226s 2 calls abc.XzFile 19.658s 1 call abc.DebDataTarFile 19.543s 1 call abc.ArFile 19.170s 40 calls abc.ElfFile 4.804s 400 calls diffoscope.comparators.elf.ElfSection 2.261s 40 calls diffoscope.comparators.elf.ElfCodeSection 1.086s 81 calls diffoscope.comparators.elf.ElfStringSection 0.027s 1 call abc.TarFile 0.005s 1 call abc.Md5sumsFile ## container_extract (total time: 0.621s) 0.524s 6 calls diffoscope.comparators.xz.XzContainer 0.037s 80 calls diffoscope.comparators.ar.ArContainer 0.035s 70 calls diffoscope.comparators.deb.DebTarContainer 0.021s 8 calls diffoscope.comparators.deb.DebContainer 0.003s 6 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 9.649s) 9.649s 6872 calls linediff ## has_same_content_as (total time: 0.059s) 0.035s 40 calls abc.ElfFile 0.017s 6 calls abc.DebFile 0.003s 1 call abc.DebDataTarFile 0.002s 400 calls diffoscope.comparators.elf.ElfSection 0.000s 81 calls diffoscope.comparators.elf.ElfStringSection 0.000s 40 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 2 calls abc.TextFile 0.000s 2 calls abc.Md5sumsFile 0.000s 2 calls abc.XzFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 1 call abc.DotChangesFile 0.000s 1 call abc.TarFile 0.000s 1 call abc.ArFile ## main (total time: 145.815s) 145.813s 2 calls outputs 0.002s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.ar.ArContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 125.120s) 125.081s 1 call html 0.021s 1 call text 0.017s 1 call json ## recognizes (total time: 1.080s) 0.620s 8800 calls diffoscope.comparators.elf.ElfSection 0.130s 3008 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.126s 1782 calls diffoscope.comparators.elf.ElfStringSection 0.090s 12 calls diffoscope.comparators.binary.FilesystemFile 0.064s 880 calls diffoscope.comparators.elf.ElfCodeSection 0.029s 324 calls diffoscope.comparators.debian.DebControlMember 0.021s 256 calls diffoscope.comparators.utils.archive.ArchiveMember 0.000s 10 calls abc.DotChangesFile 0.000s 16 calls abc.Md5sumsFile 0.000s 4 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink ## specialize (total time: 1.094s) 1.094s 578 calls specialize Mon Jan 8 21:26:10 UTC 2024 E: htslib failed to build reproducibly in bullseye on armhf. Mon Jan 8 21:26:10 UTC 2024 E: diffoscope 240 found issues, please check https://tests.reproducible-builds.org/debian/dbd/bullseye/armhf/htslib_1.11-4.diffoscope.html Mon Jan 8 21:26:12 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Jan 8 21:26:12 UTC 2024 I: Submitting 8.0K b1/htslib_1.11-4_armhf.buildinfo.asc Mon Jan 8 21:26:13 UTC 2024 I: Submitting 8.0K b2/htslib_1.11-4_armhf.buildinfo.asc Mon Jan 8 21:26:14 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jan 8 21:26:14 UTC 2024 I: Done submitting .buildinfo files. Mon Jan 8 21:26:14 UTC 2024 I: Removing signed htslib_1.11-4_armhf.buildinfo.asc files: removed './b1/htslib_1.11-4_armhf.buildinfo.asc' removed './b2/htslib_1.11-4_armhf.buildinfo.asc'