I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 2 20:20:19 -12 2024 I: pbuilder-time-stamp: 1717402819 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_1.16+ds-3.dsc] I: copying [./htslib_1.16+ds.orig.tar.bz2] I: copying [./htslib_1.16+ds-3.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Oct 19 08:47:31 2022 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./htslib_1.16+ds-3.dsc: no acceptable signature found dpkg-source: info: extracting htslib in htslib-1.16+ds dpkg-source: info: unpacking htslib_1.16+ds.orig.tar.bz2 dpkg-source: info: unpacking htslib_1.16+ds-3.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 fix_sequence_of_linked_libs.patch dpkg-source: info: applying trim-file-prefix.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1097490/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='6d321ef21c194503b0ac2b3093553d79' 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='1097490' 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.trjDVbyQ/pbuilderrc_jmuI --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.trjDVbyQ/b1 --logfile b1/build.log htslib_1.16+ds-3.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/1097490/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: amd64 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), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev; however: Package libcurl4-gnutls-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libdeflate-dev; however: Package libdeflate-dev is not installed. pbuilder-satisfydepends-dummy depends on libhtscodecs-dev (>= 1.0); however: Package libhtscodecs-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{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} libhtscodecs-dev{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{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} 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 27.2 MB of archives. After unpacking 97.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libbz2-dev amd64 1.0.8-5+b1 [30.9 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-9 [481 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs-dev amd64 1.3.0-4 [2866 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libssl-dev amd64 3.0.8-1 [2427 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Fetched 27.2 MB in 0s (81.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-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 .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../22-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../30-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../31-libbz2-dev_1.0.8-5+b1_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-5+b1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../32-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../33-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... 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Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../45-liblzma-dev_5.4.1-0.2_amd64.deb ... Unpacking liblzma-dev:amd64 (5.4.1-0.2) ... Selecting previously unselected package libssl-dev:amd64. Preparing to unpack .../46-libssl-dev_3.0.8-1_amd64.deb ... Unpacking libssl-dev:amd64 (3.0.8-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../47-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up libhtscodecs2:amd64 (1.3.0-4) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up libhtscodecs-dev:amd64 (1.3.0-4) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libssl-dev:amd64 (3.0.8-1) ... Setting up autopoint (0.21-12) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libdeflate-dev:amd64 (1.14-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libbz2-dev:amd64 (1.0.8-5+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-9) ... Setting up libcurl4-gnutls-dev:amd64 (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... 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/htslib-1.16+ds/ && 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_1.16+ds-3_source.changes dpkg-buildpackage: info: source package htslib dpkg-buildpackage: info: source version 1.16+ds-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from htslib-1.16+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/htslib-1.16+ds' dh_auto_clean make -j16 distclean make[2]: Entering directory '/build/htslib-1.16+ds' 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 -rf htscodecs/tests/test.out rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM config_vars.h version.h rm -f htscodecs/htscodecs/*.o htscodecs/htscodecs/*.pico rm -f hts-object-files rm -f htscodecs/tests/*.o rm -f libhts.a bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/pileup_mod test/plugins-dlhts test/sam test/test_bgzf test/test_expr test/test_kfunc test/test_kstring test/test_mod test/test_realn test/test-regidx test/test_str2int test/test_time_funcs test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/test_introspection test/test-bcf_set_variant_type test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7 rm -f htscodecs/tests/rans4x8 htscodecs/tests/rans4x16pr htscodecs/tests/arith_dynamic htscodecs/tests/tokenise_name3 htscodecs/tests/fqzcomp_qual htscodecs/tests/varint rm -f config.cache config.h config.log config.mk config.status rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk htscodecs.mk rm -rf autom4te.cache make[2]: Leaving directory '/build/htslib-1.16+ds' rm -rf test_backup/ make[1]: Leaving directory '/build/htslib-1.16+ds' 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/htslib-1.16+ds' # create clean copy of test dir cp -a test test_backup # to help with cross building, otherwise MMAP might get turned off export ac_cv_func_mmap_fixed_mapped=yes \ && autoconf \ && dh_auto_configure -- \ --enable-libcurl \ --enable-gcs \ --enable-s3 \ --enable-plugins \ --with-plugin-dir='/usr/lib/x86_64-linux-gnu/htslib' \ --with-external-htscodecs \ --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib' ./configure --build=x86_64-linux-gnu --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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir=/usr/lib/x86_64-linux-gnu/htslib --with-external-htscodecs --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes checking whether C compiler accepts -mavx2... yes checking whether C compiler accepts -mavx512f... yes checking whether C compiler supports ARM Neon... no 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... no checking shared library type for unknown-Linux... plain .so checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking 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 for gcc options needed to detect all undeclared functions... none needed checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing dlsym... none required checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for htscodecs/rANS_static4x16.h... yes checking for rans_compress_bound_4x16 in -lhtscodecs... yes checking for libdeflate.h... yes checking for libdeflate_deflate_compress in -ldeflate... yes checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for library containing regcomp... none required checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_external.mk to htscodecs.mk make[1]: Leaving directory '/build/htslib-1.16+ds' 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/htslib-1.16+ds' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.16" \ libdir=/usr/lib/x86_64-linux-gnu make -j16 "CFLAGS=-g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.16 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-1.16+ds' gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.16"' > version.h echo '#define HTS_CC "gcc"' > config_vars.h gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c echo '#define HTS_CPPFLAGS "-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2"' >> config_vars.h gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c echo '#define HTS_CFLAGS "-g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects"' \ | sed 's/-ffile-prefix-map=[^ ]*=.//' \ >> config_vars.h gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c echo '#define HTS_LDFLAGS "-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic"' >> config_vars.h echo '#define HTS_LIBS "-ldeflate -lhtscodecs -llzma -lbz2 -lz -lm "' >> config_vars.h gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -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 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -c -o plugin.o plugin.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_expr.pico hts_expr.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -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 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -fPIC -c -o plugin.pico plugin.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c hfile_libcurl.c: In function 'libcurl_open': hfile_libcurl.c:1335:9: warning: 'CURLINFO_CONTENT_LENGTH_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD, | ^~ In file included from hfile_libcurl.c:47: /usr/include/x86_64-linux-gnu/curl/curl.h:2858:3: note: declared here 2858 | CURLINFO_CONTENT_LENGTH_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup_mod.o test/pileup_mod.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_expr.o test/test_expr.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kfunc.o test/test_kfunc.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kstring.o test/test_kstring.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_mod.o test/test_mod.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_str2int.o test/test_str2int.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_time_funcs.o test/test_time_funcs.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_index.o test/test_index.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -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 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -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 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -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 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -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 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -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 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_introspection.o test/test_introspection.c gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc gcc -g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o gcc -shared -Wl,-soname,libhts.so.3 -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico plugin.pico -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread ln -sf libhts.so libhts.so.3 gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o plugin.o ranlib libhts.a gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread make[2]: Leaving directory '/build/htslib-1.16+ds' make[1]: Leaving directory '/build/htslib-1.16+ds' 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/htslib-1.16+ds' dh_auto_test -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.16" \ libdir=/usr/lib/x86_64-linux-gnu \ || \ if find . -name "FAIL*" > /dev/null ; then \ for file in $(find . -name "FAIL*"); do echo ${file}; cat ${file}; done && false ; \ fi make -j16 test "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 "CFLAGS=-g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.16 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-1.16+ds' test/hts_endian test/test_expr test/test_kfunc test/test_kstring test/test_str2int test/test_time_funcs test/fieldarith test/fieldarith.sam test/hfile if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ fi if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ fi test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" Expected error: [E::hts_parse_region] Unexpected string "x" after region Expected error: [E::hts_parse_region] Unexpected string "y" after region Expected error: [E::hts_parse_region] Unexpected string "chr3" after region cd test/sam_filter && ./filter.sh filter.tst Testing sam_filter... PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam |egrep -cv '^@' PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam |egrep -cv '^@' PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam |egrep -cv '^@' PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | egrep -cv '^@' PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | egrep -cv '^@' PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | egrep -cv '^@' PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | egrep -cv '^@' PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | egrep -v '^@' PASS : $tv -i 'filter=rlen<50' ../realn02.sam | egrep -v '^@' PASS : $tv -i 'filter=qlen>100' ../realn02.sam | egrep -v '^@' Expected passes: 17 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tabix && ./test-tabix.sh tabix.tst Testing tabix... PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 Expected passes: 14 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/mpileup && ./test-pileup.sh mpileup.tst Testing (m)pileup... PASS : $pileup mp_D.sam PASS : $pileup -m mp_D.sam PASS : $pileup mp_DI.sam PASS : $pileup -m mp_DI.sam PASS : $pileup mp_I.sam PASS : $pileup -m mp_I.sam PASS : $pileup mp_P.sam PASS : $pileup -m mp_P.sam PASS : $pileup mp_ID.sam PASS : $pileup -m mp_ID.sam PASS : $pileup mp_N.sam PASS : $pileup -m mp_N.sam PASS : $pileup mp_N2.sam PASS : $pileup -m mp_N2.sam PASS : $pileup c1#pad1.sam PASS : $pileup -m c1#pad1.sam PASS : $pileup c1#pad2.sam PASS : $pileup -m c1#pad2.sam PASS : $pileup c1#pad3.sam PASS : $pileup -m c1#pad3.sam PASS : $pileup -m small.bam Expected passes: 21 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/fastq && ./test-fastq.sh Testing fastq support PASS : $tview minimal.fq PASS : $tview minimal.fa PASS : $tview multiline.fq PASS : $tview multiline.fa PASS : $tview -i fastq_aux longline.fq PASS : $tview single.fq PASS : $tview single.fa PASS : $tview -i fastq_aux single.fq PASS : $tview -i fastq_aux single.fa PASS : $tview interleaved.fq PASS : $tview interleaved.fa PASS : $tview -i fastq_aux interleaved.fq PASS : $tview -i fastq_aux interleaved.fa PASS : $tview -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_casava filter_casava.fq PASS : $tview -i fastq_casava filter_casava.fa PASS : $tview -i fastq_aux r1.fq PASS : $tview -i fastq_aux r2.fq PASS : $tview -i fastq_aux r1.fa PASS : $tview -i fastq_aux r2.fa PASS : $tview -i fastq_name2 name2.fq PASS : $tview -i fastq_name2 name2.fa PASS : $tview -f minimal.sam PASS : $tview -F minimal.sam PASS : $tview -f -o fastq_aux single_aux.sam PASS : $tview -F -o fastq_aux single_aux.sam PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -f -o fastq_casava inter_casava.sam PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -F -o fastq_casava inter_casava.sam PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -f -o fastq_casava filter_casava.sam PASS : $tview -F -o fastq_casava filter_casava.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam Expected passes: 41 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/base_mods && ./base-mods.sh base-mods.tst Testing base-modifications... PASS : $test_mod MM-chebi.sam PASS : $test_mod MM-double.sam PASS : $test_mod MM-multi.sam PASS : $test_mod MM-explicit.sam PASS : $test_mod -x MM-explicit.sam PASS : $pileup_mod < MM-pileup.sam PASS : $pileup_mod < MM-pileup2.sam Expected passes: 7 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx.fa test/fastqs.fq (Expect trailing 'x' message for " -1,001x") [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] (Expect trailing 'k' message for "1.5e+3k") [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] (Expect dropped fraction message for "12.3456k") [W::hts_parse_decimal] Discarding fractional part of 12.3456k [W::hts_parse_decimal] Discarding fractional part of 12.3456k (Expect invalid numeric message for "A") [W::hts_parse_decimal] Invalid numeric value A[truncated] (Expect invalid numeric message for "G") [W::hts_parse_decimal] Invalid numeric value G[truncated] (Expect invalid numeric message for " +/-") [W::hts_parse_decimal] Invalid numeric value +/-[truncated] (Expect invalid numeric message for " -.e+9999") [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] test/test-regidx cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} 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/htslib-1.16+ds/test/test_view -l 0 -b -m 14 -x /tmp/6odlocUR40/index.bam.csi /build/htslib-1.16+ds/test/index.sam > /tmp/6odlocUR40/index.bam .. ok test_index: /build/htslib-1.16+ds/test/test_index -c /tmp/6odlocUR40/index.bam .. ok test_index: /build/htslib-1.16+ds/test/test_view -l 0 -b -m 0 -x /tmp/6odlocUR40/index.bam.bai /build/htslib-1.16+ds/test/index.sam > /tmp/6odlocUR40/index.bam .. ok test_index: /build/htslib-1.16+ds/test/test_index -b /tmp/6odlocUR40/index.bam .. ok test_index: /build/htslib-1.16+ds/test/test_view -l 0 -z -m 14 -x /tmp/6odlocUR40/index.sam.gz.csi /build/htslib-1.16+ds/test/index.sam > /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_index -c /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_view -l 0 -z -m 0 -x /tmp/6odlocUR40/index.sam.gz.bai /build/htslib-1.16+ds/test/index.sam > /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_index -b /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_view -l 0 -z -m 14 -x /tmp/6odlocUR40/index.sam.gz.csi /build/htslib-1.16+ds/test/index_dos.sam > /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_index -c /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_view -l 0 -z -m 0 -x /tmp/6odlocUR40/index.sam.gz.bai /build/htslib-1.16+ds/test/index_dos.sam > /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_index -b /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_view -l 0 -C -x /tmp/6odlocUR40/index.cram.crai /build/htslib-1.16+ds/test/index.sam > /tmp/6odlocUR40/index.cram .. ok test_index: /build/htslib-1.16+ds/test/test_index /tmp/6odlocUR40/index.cram .. ok test_index: /build/htslib-1.16+ds/test/test_view -l 0 -b -m 14 -x /tmp/6odlocUR40/index.bcf.csi /build/htslib-1.16+ds/test/index.vcf > /tmp/6odlocUR40/index.bcf .. ok test_index: /build/htslib-1.16+ds/test/test_index -c /tmp/6odlocUR40/index.bcf .. ok test_index: /build/htslib-1.16+ds/test/test_view -l 0 -z -m 14 -x /tmp/6odlocUR40/index.vcf.gz.csi /build/htslib-1.16+ds/test/index.vcf > /tmp/6odlocUR40/index.vcf.gz .. ok test_index: /build/htslib-1.16+ds/test/test_index -c /tmp/6odlocUR40/index.vcf.gz .. ok test_index: /build/htslib-1.16+ds/test/test_view -l 0 -z -m 0 -x /tmp/6odlocUR40/index.vcf.gz.tbi /build/htslib-1.16+ds/test/index.vcf > /tmp/6odlocUR40/index.vcf.gz .. ok test_index: /build/htslib-1.16+ds/test/test_index -t /tmp/6odlocUR40/index.vcf.gz .. ok test_index: /build/htslib-1.16+ds/tabix /tmp/6odlocUR40/index.vcf.gz##idx##/tmp/6odlocUR40/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/htslib-1.16+ds/test/test_view /tmp/6odlocUR40/index2.bam 1:1000000-1000000 .. ok test_index: /build/htslib-1.16+ds/test/test_view /tmp/6odlocUR40/index2.bam 1:2000000-2000000 .. ok test_index: /build/htslib-1.16+ds/test/test_view /tmp/6odlocUR40/index2.bam 2:1000000-1000000 .. ok test_index: /build/htslib-1.16+ds/test/test_view /tmp/6odlocUR40/index2.bam 2:2000000-2000000 .. ok test_index: /build/htslib-1.16+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/6odlocUR40/index.bam.csi /build/htslib-1.16+ds/test/index.sam > /tmp/6odlocUR40/index.bam .. ok test_index: /build/htslib-1.16+ds/test/test_index -c /tmp/6odlocUR40/index.bam .. ok test_index: /build/htslib-1.16+ds/test/test_view -@4 -l 0 -b -m 0 -x /tmp/6odlocUR40/index.bam.bai /build/htslib-1.16+ds/test/index.sam > /tmp/6odlocUR40/index.bam .. ok test_index: /build/htslib-1.16+ds/test/test_index -b /tmp/6odlocUR40/index.bam .. ok test_index: /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/6odlocUR40/index.sam.gz.csi /build/htslib-1.16+ds/test/index.sam > /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_index -c /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/6odlocUR40/index.sam.gz.bai /build/htslib-1.16+ds/test/index.sam > /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_index -b /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/6odlocUR40/index.sam.gz.csi /build/htslib-1.16+ds/test/index_dos.sam > /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_index -c /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/6odlocUR40/index.sam.gz.bai /build/htslib-1.16+ds/test/index_dos.sam > /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_index -b /tmp/6odlocUR40/index.sam.gz .. ok test_index: /build/htslib-1.16+ds/test/test_view -@4 -l 0 -C -x /tmp/6odlocUR40/index.cram.crai /build/htslib-1.16+ds/test/index.sam > /tmp/6odlocUR40/index.cram .. ok test_index: /build/htslib-1.16+ds/test/test_index /tmp/6odlocUR40/index.cram .. ok test_index: /build/htslib-1.16+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/6odlocUR40/index.bcf.csi /build/htslib-1.16+ds/test/index.vcf > /tmp/6odlocUR40/index.bcf .. ok test_index: /build/htslib-1.16+ds/test/test_index -c /tmp/6odlocUR40/index.bcf .. ok test_index: /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/6odlocUR40/index.vcf.gz.csi /build/htslib-1.16+ds/test/index.vcf > /tmp/6odlocUR40/index.vcf.gz .. ok test_index: /build/htslib-1.16+ds/test/test_index -c /tmp/6odlocUR40/index.vcf.gz .. ok test_index: /build/htslib-1.16+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/6odlocUR40/index.vcf.gz.tbi /build/htslib-1.16+ds/test/index.vcf > /tmp/6odlocUR40/index.vcf.gz .. ok test_index: /build/htslib-1.16+ds/test/test_index -t /tmp/6odlocUR40/index.vcf.gz .. ok test_index: /build/htslib-1.16+ds/tabix /tmp/6odlocUR40/index.vcf.gz##idx##/tmp/6odlocUR40/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/htslib-1.16+ds/test/test_view /tmp/6odlocUR40/index2.bam 1:1000000-1000000 .. ok test_index: /build/htslib-1.16+ds/test/test_view /tmp/6odlocUR40/index2.bam 1:2000000-2000000 .. ok test_index: /build/htslib-1.16+ds/test/test_view /tmp/6odlocUR40/index2.bam 2:1000000-1000000 .. ok test_index: /build/htslib-1.16+ds/test/test_view /tmp/6odlocUR40/index2.bam 2:2000000-2000000 .. ok test_view testing multi-ref CRAM modes: ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing multi-ref CRAM modes: ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out .. 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/htslib-1.16+ds/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 3.1 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [E::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out .. 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/htslib-1.16+ds/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_MD testing xx#MD.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ Checking for MD/NM in xx#MD.sam ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_MD testing xx#MD2.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_vcf_api: /build/htslib-1.16+ds/test/test-vcf-api /tmp/6odlocUR40/test-vcf-api.bcf [W::bcf_record_check] Bad BCF record at 1:1: No REF allele [E::bcf_index_build3] TBI indices for BCF files are not supported [E::idx_find_and_load] Could not retrieve index file for '/tmp/6odlocUR40/test-vcf-api.bcf' .. ok test_bcf2vcf: /build/htslib-1.16+ds/test/test_view /build/htslib-1.16+ds/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /build/htslib-1.16+ds/test/test-vcf-sweep /tmp/6odlocUR40/test-vcf-api.bcf .. ok test_vcf_various: /build/htslib-1.16+ds/htsfile -ch /build/htslib-1.16+ds/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /build/htslib-1.16+ds/htsfile -c /build/htslib-1.16+ds/test/formatcols.vcf .. ok test_vcf_various: /build/htslib-1.16+ds/htsfile -c /build/htslib-1.16+ds/test/noroundtrip.vcf .. ok test_vcf_various: /build/htslib-1.16+ds/htsfile -c /build/htslib-1.16+ds/test/formatmissing.vcf .. ok test_vcf_various: /build/htslib-1.16+ds/htsfile -c /build/htslib-1.16+ds/test/vcf_meta_meta.vcf .. ok test-bcf-sr: /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/6odlocUR40 -s 74452500 .. ok test-bcf-sr: /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/6odlocUR40 -s 34270147 .. ok test-bcf-sr: /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/6odlocUR40 -s 11108528 .. ok test-bcf-sr: /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/6odlocUR40 -s 42233895 .. ok test-bcf-sr: /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/6odlocUR40 -s 8111117 .. ok test-bcf-sr: /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/6odlocUR40 -s 85644070 .. ok test-bcf-sr: /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/6odlocUR40 -s 49879942 .. ok test-bcf-sr: /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/6odlocUR40 -s 47881429 .. ok test-bcf-sr: /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/6odlocUR40 -s 69081244 .. ok test-bcf-sr: /build/htslib-1.16+ds/test/test-bcf-sr.pl -t /tmp/6odlocUR40 -s 83459376 .. ok test_command: /build/htslib-1.16+ds/test/test-bcf-translate - .. ok test_convert_padded_header: /build/htslib-1.16+ds/test/test_view -t ce.fa -C /tmp/6odlocUR40/headernul0.bam .. ok test_convert_padded_header: /build/htslib-1.16+ds/test/test_view -t ce.fa -C /tmp/6odlocUR40/headernul1.bam .. ok test_convert_padded_header: /build/htslib-1.16+ds/test/test_view -t ce.fa -C /tmp/6odlocUR40/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /build/htslib-1.16+ds/bgzip -I /build/htslib-1.16+ds/test/bgziptest.txt.tmp.gz.gzi -c -g /build/htslib-1.16+ds/test/bgziptest.txt .. ok test-logging: /build/htslib-1.16+ds/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/build/htslib-1.16+ds /build/htslib-1.16+ds/test/with-shlib.sh /build/htslib-1.16+ds/htsfile https://localhost:99999/invalid_port .. ok test_realn: /build/htslib-1.16+ds/test/test_realn -f /build/htslib-1.16+ds/test/realn01.fa -i /build/htslib-1.16+ds/test/realn01.sam -o - .. ok test_realn: /build/htslib-1.16+ds/test/test_realn -f /build/htslib-1.16+ds/test/realn02.fa -i /build/htslib-1.16+ds/test/realn02.sam -o - .. ok test_realn: /build/htslib-1.16+ds/test/test_realn -a -f /build/htslib-1.16+ds/test/realn01.fa -i /build/htslib-1.16+ds/test/realn01.sam -o - .. ok test_realn: /build/htslib-1.16+ds/test/test_realn -a -f /build/htslib-1.16+ds/test/realn02.fa -i /build/htslib-1.16+ds/test/realn02.sam -o - .. ok test_realn: /build/htslib-1.16+ds/test/test_realn -e -f /build/htslib-1.16+ds/test/realn01.fa -i /build/htslib-1.16+ds/test/realn01.sam -o - .. ok test_realn: /build/htslib-1.16+ds/test/test_realn -e -f /build/htslib-1.16+ds/test/realn02.fa -i /build/htslib-1.16+ds/test/realn02.sam -o - .. ok test_realn: /build/htslib-1.16+ds/test/test_realn -r -f /build/htslib-1.16+ds/test/realn02.fa -i /build/htslib-1.16+ds/test/realn02-r.sam -o - .. ok test_realn: /build/htslib-1.16+ds/test/test_realn -a -f /build/htslib-1.16+ds/test/realn02.fa -i /build/htslib-1.16+ds/test/realn02_exp.sam -o - .. ok test_realn: /build/htslib-1.16+ds/test/test_realn -f /build/htslib-1.16+ds/test/realn02.fa -i /build/htslib-1.16+ds/test/realn02_exp-a.sam -o - .. ok test-bcf_set_variant_type: /build/htslib-1.16+ds/test/test-bcf_set_variant_type .. ok Number of tests: total .. 174 passed .. 174 failed .. 0 make[2]: Leaving directory '/build/htslib-1.16+ds' rm -fr -- /tmp/dh-xdg-rundir-VUmqGN8H make[1]: Leaving directory '/build/htslib-1.16+ds' 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/htslib-1.16+ds' echo "Suppress test for Architecture independant builds." Suppress test for Architecture independant builds. make[1]: Leaving directory '/build/htslib-1.16+ds' 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/htslib-1.16+ds' for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \ rm /build/htslib-1.16+ds/test/${binary} ; \ done dh_auto_install -- prefix=/usr \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.16" \ libdir=/usr/lib/x86_64-linux-gnu install -m0755 -d /build/htslib-1.16\+ds/debian/tmp make -j16 install DESTDIR=/build/htslib-1.16\+ds/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr "CFLAGS=-g -O2 -ffile-prefix-map=/build/htslib-1.16+ds=. -fstack-protector-strong -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.16 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-1.16+ds' mkdir -p -m 755 /build/htslib-1.16+ds/debian/tmp/usr/bin /build/htslib-1.16+ds/debian/tmp/usr/include /build/htslib-1.16+ds/debian/tmp/usr/include/htslib /build/htslib-1.16+ds/debian/tmp/usr/lib/x86_64-linux-gnu /build/htslib-1.16+ds/debian/tmp/usr/share/man/man1 /build/htslib-1.16+ds/debian/tmp/usr/share/man/man5 /build/htslib-1.16+ds/debian/tmp/usr/share/man/man7 /build/htslib-1.16+ds/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig if test -n "/usr/lib/x86_64-linux-gnu/htslib"; then mkdir -p -m 755 /build/htslib-1.16+ds/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 libhts.so /build/htslib-1.16+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.16 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/x86_64-linux-gnu#g;s#@-PACKAGE_VERSION@#1.16#g' htslib.pc.tmp > /build/htslib-1.16+ds/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc chmod 644 /build/htslib-1.16+ds/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc ln -sf libhts.so.1.16 /build/htslib-1.16+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so ln -sf libhts.so.1.16 /build/htslib-1.16+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.3 install -p bgzip htsfile tabix /build/htslib-1.16+ds/debian/tmp/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /build/htslib-1.16+ds/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 htslib/*.h /build/htslib-1.16+ds/debian/tmp/usr/include/htslib install -p -m 644 libhts.a /build/htslib-1.16+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a install -p -m 644 bgzip.1 htsfile.1 tabix.1 /build/htslib-1.16+ds/debian/tmp/usr/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /build/htslib-1.16+ds/debian/tmp/usr/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /build/htslib-1.16+ds/debian/tmp/usr/share/man/man7 make[2]: Leaving directory '/build/htslib-1.16+ds' # restore clean copy of test dir before dh_install is run # This should not be done earlier since dh_auto_install contains some unconditional removals rm -f -r test mv test_backup test make[1]: Leaving directory '/build/htslib-1.16+ds' 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/htslib-1.16+ds' dh_install --indep install -m0755 -d debian/htslib-test/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/tests/run-unit-test debian/htslib-test/usr/share/doc/libhts-dev/ install -m0755 -d debian/htslib-test/usr/share/htslib-test cp --reflink=auto -a ./Makefile ./bcf_sr_sort.c ./bcf_sr_sort.h ./bgzf.c ./bgzip.c ./config.h ./config.mk ./config_vars.h ./errmod.c ./faidx.c ./header.c ./header.h ./hfile.c ./hfile_gcs.c ./hfile_internal.h ./hfile_libcurl.c ./hfile_s3.c ./hfile_s3_write.c ./hts.c ./hts_expr.c ./hts_internal.h ./hts_os.c ./hts_time_funcs.h ./htscodecs.mk ./htscodecs_bundled.mk ./htscodecs_external.mk ./htsfile.c ./htslib.mk ./htslib_static.mk ./htslib_vars.mk ./kfunc.c ./kstring.c ./md5.c ./multipart.c ./os ./plugin.c ./probaln.c ./realn.c ./regidx.c ./region.c ./sam.c ./sam_internal.h ./synced_bcf_reader.c ./tabix.c ./tbx.c ./textutils.c ./textutils_internal.h ./thread_pool.c ./thread_pool_internal.h ./vcf.c ./vcf_sweep.c ./vcfutils.c ./version.h ./version.sh debian/htslib-test/usr/share/htslib-test/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/cram cp --reflink=auto -a ./cram/cram.h ./cram/cram_codecs.c ./cram/cram_codecs.h ./cram/cram_decode.c ./cram/cram_decode.h ./cram/cram_encode.c ./cram/cram_encode.h ./cram/cram_external.c ./cram/cram_index.c ./cram/cram_index.h ./cram/cram_io.c ./cram/cram_io.h ./cram/cram_samtools.h ./cram/cram_stats.c ./cram/cram_stats.h ./cram/cram_structs.h ./cram/mFILE.c ./cram/mFILE.h ./cram/misc.h ./cram/open_trace_file.c ./cram/open_trace_file.h ./cram/os.h ./cram/pooled_alloc.c ./cram/pooled_alloc.h ./cram/string_alloc.c ./cram/string_alloc.h debian/htslib-test/usr/share/htslib-test/cram/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/test cp --reflink=auto -a ./test/auxf\#values.sam ./test/auxf\#values_java.cram ./test/auxf.fa ./test/auxf.fa.fai ./test/base_mods ./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/fastq ./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/index2.sam ./test/index_dos.sam ./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/pileup_mod.c ./test/plugins-dlhts.c ./test/range.bam ./test/range.bam.bai ./test/range.cram ./test/range.cram.crai ./test/range.out ./test/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/sam_filter ./test/simple_test_driver.sh ./test/tabix ./test/tabix.out ./test/test-bcf-sr.c ./test/test-bcf-sr.pl ./test/test-bcf-translate.c ./test/test-bcf-translate.out ./test/test-bcf_set_variant_type.c ./test/test-logging.pl ./test/test-parse-reg.c ./test/test-regidx.c ./test/test-vcf-api.c ./test/test-vcf-api.out ./test/test-vcf-hdr-in.vcf ./test/test-vcf-hdr.out ./test/test-vcf-sweep.c ./test/test-vcf-sweep.out ./test/test.pl ./test/test_bgzf.c ./test/test_expr.c ./test/test_index.c ./test/test_introspection.c ./test/test_kfunc.c ./test/test_kstring.c ./test/test_mod.c ./test/test_realn.c ./test/test_str2int.c ./test/test_time_funcs.c ./test/test_view.c ./test/thrash_threads1.c ./test/thrash_threads2.c ./test/thrash_threads3.c ./test/thrash_threads4.c ./test/thrash_threads5.c ./test/thrash_threads6.c ./test/thrash_threads7.c ./test/thread_pool.md ./test/vcf_meta_meta.vcf ./test/with-shlib.sh ./test/xx\#MD.sam ./test/xx\#MD2.sam ./test/xx\#blank.sam ./test/xx\#large_aux.sam ./test/xx\#large_aux2.sam ./test/xx\#large_aux_java.cram ./test/xx\#minimal.sam ./test/xx\#pair.sam ./test/xx\#repeated.sam ./test/xx\#rg.sam ./test/xx\#tlen.sam ./test/xx\#tlen2.sam ./test/xx\#triplet.sam ./test/xx\#unsorted.sam ./test/xx.fa ./test/xx.fa.fai debian/htslib-test/usr/share/htslib-test/test/ sed -i 's/-ffile-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk sed -i 's/-fdebug-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk sed -i 's#\.\./\.\./htslib/#htslib/#' `grep -Rl '../../htslib/' debian/htslib-test/*` make[1]: Leaving directory '/build/htslib-1.16+ds' dh_install -Nhtslib-test install -m0755 -d debian/libhts3/usr/lib/x86_64-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/htslib debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.16 debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.3 debian/libhts3/usr/lib/x86_64-linux-gnu/ install -m0755 -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 -m0755 -d debian/libhts-dev/usr/include cp --reflink=auto -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/ install -m0755 -d debian/libhts-dev/usr/lib/x86_64-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so debian/libhts-dev/usr/lib/x86_64-linux-gnu/ install -m0755 -d debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig/ install -m0755 -d debian/tabix/usr/bin cp --reflink=auto -a ./bgzip ./htsfile ./tabix debian/tabix/usr/bin/ rm -f debian/htslib-test.debhelper.log debian/rules override_dh_installdocs make[1]: Entering directory '/build/htslib-1.16+ds' dh_installdocs install -m0755 -d debian/libhts3/usr/share/doc/libhts3 install -p -m0644 debian/copyright debian/libhts3/usr/share/doc/libhts3/copyright install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/README.test debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README.large_positions.md debian/libhts-dev/usr/share/doc/libhts-dev chmod -R u\+rw,go=rX debian/libhts-dev/usr/share/doc install -p -m0644 debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/copyright debian/htslib-test/usr/share/doc/htslib-test/copyright install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright # Fix Perl interpreter path for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so: No such file or directory make[1]: Leaving directory '/build/htslib-1.16+ds' 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/htslib-1.16+ds' dh_installchangelogs NEWS install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -p -m0644 debian/.debhelper/generated/libhts-dev/dh_installchangelogs.dch.trimmed debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog install -m0755 -d debian/libhts3/usr/share/doc/libhts3 install -p -m0644 debian/.debhelper/generated/libhts3/dh_installchangelogs.dch.trimmed debian/libhts3/usr/share/doc/libhts3/changelog.Debian install -p -m0644 NEWS debian/libhts3/usr/share/doc/libhts3/changelog install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/.debhelper/generated/htslib-test/dh_installchangelogs.dch.trimmed debian/htslib-test/usr/share/doc/htslib-test/changelog.Debian install -p -m0644 NEWS debian/htslib-test/usr/share/doc/htslib-test/changelog install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/.debhelper/generated/tabix/dh_installchangelogs.dch.trimmed debian/tabix/usr/share/doc/tabix/changelog.Debian install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog make[1]: Leaving directory '/build/htslib-1.16+ds' dh_installman install -m0755 -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 -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./htsfile.1 debian/tabix/usr/share/man/man1/htsfile.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./tabix.1 debian/tabix/usr/share/man/man1/tabix.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./bgzip.1 debian/tabix/usr/share/man/man1/bgzip.1 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man5/faidx.5 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man5/sam.5 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/bgzip.1 man-recode --to-code UTF-8 --suffix .dh-new 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 chmod 0644 -- 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 chmod 0644 -- debian/libhts3/usr/share/man/man5/sam.5 mv debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7 chmod 0644 -- debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7 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/vcf.5 mv debian/tabix/usr/share/man/man1/bgzip.1.dh-new debian/tabix/usr/share/man/man1/bgzip.1 chmod 0644 -- debian/tabix/usr/share/man/man1/bgzip.1 mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1 chmod 0644 -- debian/tabix/usr/share/man/man1/htsfile.1 mv debian/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1 chmod 0644 -- debian/tabix/usr/share/man/man1/tabix.1 dh_lintian install -m0755 -d debian/htslib-test/usr/share/lintian/overrides install -p -m0644 debian/htslib-test.lintian-overrides debian/htslib-test/usr/share/lintian/overrides/htslib-test dh_perl mv debian/htslib-test.substvars.new debian/htslib-test.substvars dh_link rm -f debian/libhts3/usr/lib/x86_64-linux-gnu/libhts.so.3 ln -s libhts.so.1.16 debian/libhts3/usr/lib/x86_64-linux-gnu/libhts.so.3 rm -f debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so ln -s libhts.so.1.16 debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so rm -f debian/htslib-test/usr/share/htslib-test/htscodecs.mk ln -s htscodecs_external.mk debian/htslib-test/usr/share/htslib-test/htscodecs.mk install -m0755 -d debian/tabix/usr/share/man/man1 rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz ln -s tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz dh_strip_nondeterminism dh_compress cd debian/libhts3 cd debian/libhts-dev cd debian/htslib-test cd debian/tabix 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 chmod a-x usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 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/htslib-test/changelog usr/share/doc/htslib-test/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 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 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/htslib-1.16+ds' cd '/build/htslib-1.16+ds' cd '/build/htslib-1.16+ds' cd '/build/htslib-1.16+ds' 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/htslib-1.16+ds' 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/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/htslib-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/tabix ! -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/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/doc -type f -a -true -a ! -regex 'debian/htslib-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts3/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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/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/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w 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/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/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian -name simple_test_driver.sh -exec chmod +x \{\} \; make[1]: Leaving directory '/build/htslib-1.16+ds' 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/htslib-1.16+ds' # FIXME: No idea why these files are remaining in debian/tmp rm -rf debian/tmp/usr/bin debian/tmp/usr/share/man dh_missing make[1]: Leaving directory '/build/htslib-1.16+ds' dh_dwz -a install -m0755 -d debian/libhts3/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/libhts3/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3.debug -- debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/libhts3/usr/lib/x86_64-linux-gnu/libhts.so.1.16 install -m0755 -d debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix dwz: debian/libhts3/usr/lib/x86_64-linux-gnu/libhts.so.1.16: DWARF compression not beneficial - old size 910589 new size 932008 objcopy --compress-debug-sections debian/libhts3/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3.debug chmod 0644 -- debian/libhts3/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3.debug objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug chmod 0644 -- debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/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/htslib-1.16+ds' # This is apparently important for the interpretation by ldc2 in sambamba dh_strip -Xlibhts.a install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/31 objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/x86_64-linux-gnu/libhts.so.1.16 debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/31/c0046a3119d307dd7fb3280bc45c45c5fe4ccc.debug install -m0755 -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/e6/6b3d6cd9299d472d1bfd9dc0b33fcc407e26ed.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/e6/6b3d6cd9299d472d1bfd9dc0b33fcc407e26ed.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/e6/6b3d6cd9299d472d1bfd9dc0b33fcc407e26ed.debug debian/tabix/usr/bin/htsfile chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/31/c0046a3119d307dd7fb3280bc45c45c5fe4ccc.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/x86_64-linux-gnu/libhts.so.1.16 objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/31/c0046a3119d307dd7fb3280bc45c45c5fe4ccc.debug debian/libhts3/usr/lib/x86_64-linux-gnu/libhts.so.1.16 install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/ec objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/ec/f0840ee5781cc14646dc6b307b6cbf7d023d4e.debug install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/6e objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/6e/ed7d9a9590673f3d342b245f25db13b134c773.debug chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/6e/ed7d9a9590673f3d342b245f25db13b134c773.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/6e/ed7d9a9590673f3d342b245f25db13b134c773.debug debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/61 objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/61/5e51c67ffeef4b340e21bc3091a562514ea377.debug chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/61/5e51c67ffeef4b340e21bc3091a562514ea377.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/61/5e51c67ffeef4b340e21bc3091a562514ea377.debug debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/0c objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/0c/da90fa488a94e89fe9dfa91c9e016903b6d6a1.debug chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/0c/da90fa488a94e89fe9dfa91c9e016903b6d6a1.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/0c/da90fa488a94e89fe9dfa91c9e016903b6d6a1.debug debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/12 objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/12/9e9e505ddf6033f046fc3fb56169a56c415938.debug chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/12/9e9e505ddf6033f046fc3fb56169a56c415938.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/12/9e9e505ddf6033f046fc3fb56169a56c415938.debug debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/libhts3/usr/lib/debug/.dwz/x86_64-linux-gnu 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 -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/share/doc ln -s libhts3 debian/.debhelper/libhts3/dbgsym-root/usr/share/doc/libhts3-dbgsym install -m0755 -d debian/.debhelper/libhts3 chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/ec/f0840ee5781cc14646dc6b307b6cbf7d023d4e.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/tabix objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/ec/f0840ee5781cc14646dc6b307b6cbf7d023d4e.debug debian/tabix/usr/bin/tabix install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cc objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cc/1fd2bd244feb6d7962af62af1152878fa4cf71.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cc/1fd2bd244feb6d7962af62af1152878fa4cf71.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/cc/1fd2bd244feb6d7962af62af1152878fa4cf71.debug debian/tabix/usr/bin/bgzip install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/tabix/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/tabix/usr/lib/debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym install -m0755 -d debian/.debhelper/tabix make[1]: Leaving directory '/build/htslib-1.16+ds' dh_makeshlibs -a rm -f debian/libhts3/DEBIAN/shlibs install -m0755 -d debian/libhts3/DEBIAN echo "libhts 3 libhts3 (>= 1.16+ds)" >> debian/libhts3/DEBIAN/shlibs chmod 0644 -- debian/libhts3/DEBIAN/shlibs dpkg-gensymbols -plibhts3 -Idebian/libhts3.symbols -Pdebian/libhts3 -edebian/libhts3/usr/lib/x86_64-linux-gnu/libhts.so.1.16 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 -m0755 -d debian/tabix/DEBIAN dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix debian/tabix/usr/bin/bgzip install -m0755 -d debian/libhts3/DEBIAN dpkg-shlibdeps -Tdebian/libhts3.substvars debian/libhts3/usr/lib/x86_64-linux-gnu/libhts.so.1.16 debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/libhts3/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so dh_installdeb install -m0755 -d debian/libhts3/DEBIAN install -p -m0644 debian/.debhelper/generated/libhts3/triggers debian/libhts3/DEBIAN/triggers install -m0755 -d debian/libhts-dev/DEBIAN install -m0755 -d debian/htslib-test/DEBIAN install -m0755 -d debian/tabix/DEBIAN dh_gencontrol install -m0755 -d debian/libhts-dev/DEBIAN echo misc:Depends= >> debian/libhts-dev.substvars echo misc:Pre-Depends= >> debian/libhts-dev.substvars dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -Pdebian/libhts-dev install -m0755 -d debian/libhts3/DEBIAN echo misc:Depends= >> debian/libhts3.substvars echo misc:Pre-Depends= >> debian/libhts3.substvars install -m0755 -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=0cda90fa488a94e89fe9dfa91c9e016903b6d6a1 129e9e505ddf6033f046fc3fb56169a56c415938 31c0046a3119d307dd7fb3280bc45c45c5fe4ccc 615e51c67ffeef4b340e21bc3091a562514ea377 6eed7d9a9590673f3d342b245f25db13b134c773" -DSection=debug -UReplaces -UBreaks install -m0755 -d debian/tabix/DEBIAN echo misc:Depends= >> debian/tabix.substvars echo misc:Pre-Depends= >> debian/tabix.substvars install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -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=cc1fd2bd244feb6d7962af62af1152878fa4cf71 e66b3d6cd9299d472d1bfd9dc0b33fcc407e26ed ecf0840ee5781cc14646dc6b307b6cbf7d023d4e" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/htslib-test/DEBIAN echo misc:Depends= >> debian/htslib-test.substvars echo misc:Pre-Depends= >> debian/htslib-test.substvars dpkg-gencontrol -phtslib-test -ldebian/changelog -Tdebian/htslib-test.substvars -Pdebian/htslib-test chmod 0644 -- debian/libhts-dev/DEBIAN/control 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 chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix chmod 0644 -- debian/libhts3/DEBIAN/control chmod 0644 -- debian/tabix/DEBIAN/control dh_md5sums install -m0755 -d debian/libhts3/DEBIAN install -m0755 -d debian/tabix/DEBIAN install -m0755 -d debian/libhts-dev/DEBIAN install -m0755 -d debian/htslib-test/DEBIAN cd debian/tabix >/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 cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/htslib-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts3/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/DEBIAN chmod 0644 -- debian/tabix/DEBIAN/md5sums install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN cd debian/.debhelper/libhts3/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/htslib-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/libhts3 .. dpkg-deb --root-owner-group --build debian/.debhelper/libhts3/dbgsym-root .. dpkg-deb --root-owner-group --build debian/libhts-dev .. dpkg-deb --root-owner-group --build debian/htslib-test .. dpkg-deb --root-owner-group --build debian/tabix .. dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root .. dpkg-deb: building package 'libhts3' in '../libhts3_1.16+ds-3_amd64.deb'. dpkg-deb: building package 'libhts3-dbgsym' in '../libhts3-dbgsym_1.16+ds-3_amd64.deb'. dpkg-deb: building package 'htslib-test' in '../htslib-test_1.16+ds-3_all.deb'. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.16+ds-3_amd64.deb'. dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.16+ds-3_amd64.deb'. dpkg-deb: building package 'tabix' in '../tabix_1.16+ds-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../htslib_1.16+ds-3_amd64.buildinfo dpkg-genchanges --build=binary -O../htslib_1.16+ds-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from htslib-1.16+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/1097490 and its subdirectories I: Current time: Sun Jun 2 20:22:16 -12 2024 I: pbuilder-time-stamp: 1717402936