https://launchpad.net/ubuntu/+source/htslib/1.9-6/+build/15744970 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-047 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 6 Dec 11:09:02 ntpdate[1804]: adjust time server 10.211.37.1 offset 0.092325 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15744970 /home/buildd/filecache-default/b71572c9405b6ce6ff1d1ad001cf764bb07f52ae Creating target for build PACKAGEBUILD-15744970 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15744970 Starting target for build PACKAGEBUILD-15744970 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15744970 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15744970 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15744970 Updating target for build PACKAGEBUILD-15744970 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main amd64 Packages [1004 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe amd64 Packages [8928 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5134 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 Packages [86.0 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [43.8 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 Packages [320 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [167 kB] Fetched 16.7 MB in 5s (3698 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libgdbm6 libperl5.28 perl-modules-5.28 The following packages will be upgraded: apt base-files binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-8 dash dmsetup dpkg dpkg-dev fakeroot findutils g++ g++-8 gcc gcc-8 gcc-8-base grep hostname init init-system-helpers libapparmor1 libapt-pkg5.0 libasan5 libatomic1 libaudit-common libaudit1 libbinutils libcap-ng0 libcc1-0 libdb5.3 libdevmapper1.02.1 libdpkg-perl libfakeroot libffi6 libgcc-8-dev libgcc1 libgcrypt20 libgdbm-compat4 libgmp10 libgnutls30 libgomp1 libgpg-error0 libhogweed4 libitm1 libkmod2 liblsan0 libmpx2 libnettle6 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsqlite3-0 libssl1.1 libstdc++-8-dev libstdc++6 libsystemd0 libtsan0 libubsan1 libudev1 linux-libc-dev lockfile-progs openssl perl perl-base sed systemd systemd-sysv tar tzdata 73 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 54.7 MB of archives. After this operation, 48.9 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main amd64 base-files amd64 10.1ubuntu8 [60.1 kB] Get:2 http://ftpmaster.internal/ubuntu disco/main amd64 tar amd64 1.30+dfsg-3 [242 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main amd64 dpkg amd64 1.19.2ubuntu1 [1101 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main amd64 dash amd64 0.5.10.2-1 [89.3 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main amd64 findutils amd64 4.6.0+git+20181018-1 [295 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main amd64 grep amd64 3.1-3 [152 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main amd64 hostname amd64 3.21 [11.2 kB] Get:8 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 perl-modules-5.28 all 5.28.1-2 [2812 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main amd64 libgdbm6 amd64 1.18.1-2 [27.6 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main amd64 libgdbm-compat4 amd64 1.18.1-2 [6152 B] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libperl5.28 amd64 5.28.1-2 [3830 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 perl amd64 5.28.1-2 [204 kB] Get:13 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 perl-base amd64 5.28.1-2 [1511 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.2 [672 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main amd64 sed amd64 4.5-2 [186 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main amd64 init-system-helpers all 1.56 [38.8 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main amd64 libquadmath0 amd64 8.2.0-10ubuntu1 [134 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main amd64 libubsan1 amd64 8.2.0-10ubuntu1 [121 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main amd64 gcc-8-base amd64 8.2.0-10ubuntu1 [18.7 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main amd64 libgcc1 amd64 1:8.2.0-10ubuntu1 [40.8 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main amd64 libitm1 amd64 8.2.0-10ubuntu1 [28.2 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main amd64 libasan5 amd64 8.2.0-10ubuntu1 [364 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main amd64 libgomp1 amd64 8.2.0-10ubuntu1 [76.4 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main amd64 libatomic1 amd64 8.2.0-10ubuntu1 [9060 B] Get:25 http://ftpmaster.internal/ubuntu disco/main amd64 liblsan0 amd64 8.2.0-10ubuntu1 [132 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main amd64 libtsan0 amd64 8.2.0-10ubuntu1 [288 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main amd64 libmpx2 amd64 8.2.0-10ubuntu1 [11.7 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main amd64 cpp-8 amd64 8.2.0-10ubuntu1 [7222 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main amd64 libcc1-0 amd64 8.2.0-10ubuntu1 [39.5 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main amd64 gcc-8 amd64 8.2.0-10ubuntu1 [8000 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main amd64 g++-8 amd64 8.2.0-10ubuntu1 [8116 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main amd64 libstdc++-8-dev amd64 8.2.0-10ubuntu1 [1539 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main amd64 libgcc-8-dev amd64 8.2.0-10ubuntu1 [2305 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main amd64 libstdc++6 amd64 8.2.0-10ubuntu1 [400 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main amd64 libgmp10 amd64 2:6.1.2+dfsg-4 [236 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main amd64 libbinutils amd64 2.31.1-10ubuntu1 [482 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main amd64 binutils-common amd64 2.31.1-10ubuntu1 [194 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main amd64 binutils amd64 2.31.1-10ubuntu1 [3396 B] Get:39 http://ftpmaster.internal/ubuntu disco/main amd64 binutils-x86-64-linux-gnu amd64 2.31.1-10ubuntu1 [1830 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main amd64 libudev1 amd64 239-7ubuntu15 [54.7 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main amd64 libapt-pkg5.0 amd64 1.8.0~alpha2ubuntu1 [814 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main amd64 libnettle6 amd64 3.4.1~rc1-1 [111 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main amd64 libhogweed4 amd64 3.4.1~rc1-1 [140 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main amd64 libgnutls30 amd64 3.6.4-2ubuntu2 [747 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main amd64 libseccomp2 amd64 2.3.3-3ubuntu2 [38.9 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main amd64 apt amd64 1.8.0~alpha2ubuntu1 [1182 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main amd64 systemd-sysv amd64 239-7ubuntu15 [9396 B] Get:48 http://ftpmaster.internal/ubuntu disco/main amd64 libapparmor1 amd64 2.12-4ubuntu10 [29.9 kB] Get:49 http://ftpmaster.internal/ubuntu disco/main amd64 libaudit-common all 1:2.8.3-1ubuntu3 [4068 B] Get:50 http://ftpmaster.internal/ubuntu disco/main amd64 libcap-ng0 amd64 0.7.9-1build1 [10.9 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main amd64 libaudit1 amd64 1:2.8.3-1ubuntu3 [38.8 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main amd64 libgpg-error0 amd64 1.32-3 [56.0 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main amd64 libkmod2 amd64 25-1ubuntu2 [41.7 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main amd64 systemd amd64 239-7ubuntu15 [2971 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main amd64 libsystemd0 amd64 239-7ubuntu15 [212 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main amd64 init amd64 1.56 [6652 B] Get:57 http://ftpmaster.internal/ubuntu disco/main amd64 libgcrypt20 amd64 1.8.4-3ubuntu1 [420 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main amd64 libselinux1 amd64 2.8-1build2 [68.6 kB] Get:59 http://ftpmaster.internal/ubuntu disco/main amd64 libsemanage-common all 2.8-1build2 [6892 B] Get:60 http://ftpmaster.internal/ubuntu disco/main amd64 libsemanage1 amd64 2.8-1build2 [85.1 kB] Get:61 http://ftpmaster.internal/ubuntu disco/main amd64 libffi6 amd64 3.2.1-9 [18.1 kB] Get:62 http://ftpmaster.internal/ubuntu disco/main amd64 libdevmapper1.02.1 amd64 2:1.02.145-4.1ubuntu4 [127 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main amd64 dmsetup amd64 2:1.02.145-4.1ubuntu4 [74.6 kB] Get:64 http://ftpmaster.internal/ubuntu disco/main amd64 libsqlite3-0 amd64 3.26.0-1 [530 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main amd64 libssl1.1 amd64 1.1.1a-1ubuntu2 [1297 kB] Get:66 http://ftpmaster.internal/ubuntu disco/main amd64 openssl amd64 1.1.1a-1ubuntu2 [618 kB] Get:67 http://ftpmaster.internal/ubuntu disco/main amd64 tzdata all 2018g-1 [188 kB] Get:68 http://ftpmaster.internal/ubuntu disco/main amd64 g++ amd64 4:8.2.0-2ubuntu2 [1608 B] Get:69 http://ftpmaster.internal/ubuntu disco/main amd64 gcc amd64 4:8.2.0-2ubuntu2 [5224 B] Get:70 http://ftpmaster.internal/ubuntu disco/main amd64 cpp amd64 4:8.2.0-2ubuntu2 [27.6 kB] Get:71 http://ftpmaster.internal/ubuntu disco/main amd64 dpkg-dev all 1.19.2ubuntu1 [549 kB] Get:72 http://ftpmaster.internal/ubuntu disco/main amd64 libdpkg-perl all 1.19.2ubuntu1 [227 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main amd64 libfakeroot amd64 1.23-1 [25.3 kB] Get:74 http://ftpmaster.internal/ubuntu disco/main amd64 fakeroot amd64 1.23-1 [62.4 kB] Get:75 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 linux-libc-dev amd64 4.19.0-7.8 [1043 kB] Get:76 http://ftpmaster.internal/ubuntu disco/main amd64 lockfile-progs amd64 0.1.18 [9872 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 54.7 MB in 1s (53.7 MB/s) (Reading database ... 12650 files and directories currently installed.) 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Preparing to unpack .../dash_0.5.10.2-1_amd64.deb ... dpkg-divert: warning: please specify --no-rename explicitly, the default will change to --rename in 1.20.x Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' dpkg-divert: warning: please specify --no-rename explicitly, the default will change to --rename in 1.20.x Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' dpkg-divert: warning: please specify --no-rename explicitly, the default will change to --rename in 1.20.x Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' dpkg-divert: warning: please specify --no-rename explicitly, the default will change to --rename in 1.20.x Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' Unpacking dash (0.5.10.2-1) over (0.5.8-2.10) ... 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Setting up libgcc-8-dev:amd64 (8.2.0-10ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.31.1-10ubuntu1) ... Setting up libstdc++-8-dev:amd64 (8.2.0-10ubuntu1) ... Setting up libdpkg-perl (1.19.2ubuntu1) ... Setting up binutils (2.31.1-10ubuntu1) ... Setting up gcc-8 (8.2.0-10ubuntu1) ... Setting up g++-8 (8.2.0-10ubuntu1) ... Setting up dpkg-dev (1.19.2ubuntu1) ... Setting up gcc (4:8.2.0-2ubuntu2) ... Setting up g++ (4:8.2.0-2ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15744970 amd64 disco-proposed -c chroot:build-PACKAGEBUILD-15744970 --arch=amd64 --dist=disco-proposed --nolog -A htslib_1.9-6.dsc Initiating build PACKAGEBUILD-15744970 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-047.buildd +==============================================================================+ | htslib 1.9-6 (amd64) 06 Dec 2018 11:09 | +==============================================================================+ Package: htslib Version: 1.9-6 Source Version: 1.9-6 Distribution: disco-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/htslib-sPtCjU/htslib-1.9' with '<>' I: NOTICE: Log filtering will replace 'build/htslib-sPtCjU' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15744970/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- htslib_1.9-6.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-sH_KBD/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-sH_KBD/apt_archive ./ InRelease Get:2 copy:/<>/resolver-sH_KBD/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-sH_KBD/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-sH_KBD/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-sH_KBD/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (252 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-sH_KBD/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14507 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev Filtered Build-Depends: debhelper (>= 11~), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-htslib-dummy' in '/<>/resolver-TNyxac/apt_archive/sbuild-build-depends-htslib-dummy.deb'. Ign:1 copy:/<>/resolver-TNyxac/apt_archive ./ InRelease Get:2 copy:/<>/resolver-TNyxac/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-TNyxac/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-TNyxac/apt_archive ./ Sources [252 B] Get:5 copy:/<>/resolver-TNyxac/apt_archive ./ Packages [570 B] Fetched 2941 B in 0s (266 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install htslib build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libicu63 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssl-dev libtool libwind0-heimdal libxml2 m4 man-db po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config krb5-doc krb5-user liblzma-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libicu63 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssl-dev libtool libwind0-heimdal libxml2 m4 man-db po-debconf sbuild-build-depends-htslib-dummy zlib1g-dev 0 upgraded, 59 newly installed, 0 to remove and 0 not upgraded. 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amd64 0.12-2 [77.7 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main amd64 libcroco3 amd64 0.6.12-2 [81.3 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main amd64 gettext amd64 0.19.8.1-9 [896 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main amd64 po-debconf all 1.0.21 [233 kB] Get:37 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 debhelper all 11.5.3ubuntu1 [888 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main amd64 libroken18-heimdal amd64 7.5.0+dfsg-2.1 [41.4 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main amd64 libasn1-8-heimdal amd64 7.5.0+dfsg-2.1 [182 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main amd64 libbz2-dev amd64 1.0.6-9 [30.2 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main amd64 libheimbase1-heimdal amd64 7.5.0+dfsg-2.1 [29.4 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main amd64 libhcrypto4-heimdal amd64 7.5.0+dfsg-2.1 [86.7 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main amd64 libwind0-heimdal amd64 7.5.0+dfsg-2.1 [47.8 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main amd64 libhx509-5-heimdal amd64 7.5.0+dfsg-2.1 [107 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main amd64 libkrb5-26-heimdal amd64 7.5.0+dfsg-2.1 [206 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main amd64 libheimntlm0-heimdal amd64 7.5.0+dfsg-2.1 [14.8 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main amd64 libgssapi3-heimdal amd64 7.5.0+dfsg-2.1 [96.4 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [14.8 kB] Get:49 http://ftpmaster.internal/ubuntu disco/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [49.2 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main amd64 libldap-common all 2.4.46+dfsg-5ubuntu3 [16.0 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main amd64 libldap-2.4-2 amd64 2.4.46+dfsg-5ubuntu3 [154 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main amd64 libnghttp2-14 amd64 1.35.0-1 [78.9 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [54.5 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main amd64 libcurl3-gnutls amd64 7.61.0-1ubuntu2.2 [215 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main amd64 libcurl4-gnutls-dev amd64 7.61.0-1ubuntu2.2 [297 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main amd64 libssl-dev amd64 1.1.1a-1ubuntu2 [1569 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-0ubuntu2 [176 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main amd64 dh-exec amd64 0.23build1 [24.6 kB] Get:59 http://ftpmaster.internal/ubuntu disco/main amd64 liblzma-dev amd64 5.2.2-1.3 [145 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 21.1 MB in 0s (53.1 MB/s) Selecting previously unselected package libbsd0:amd64. 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Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libpipeline1:amd64 (1.5.0-2) ... Setting up libroken18-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up m4 (1.4.18-2) ... Setting up libbsd0:amd64 (0.9.1-1) ... Setting up libkrb5support0:amd64 (1.16.1-1ubuntu1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7ubuntu3) ... Setting up libmagic-mgc (1:5.34-2) ... Setting up libmagic1:amd64 (1:5.34-2) ... Setting up libcroco3:amd64 (0.6.12-2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up dwz (0.12-2) ... Setting up autotools-dev (20180224.1) ... Setting up libheimbase1-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up liblzma-dev:amd64 (5.2.2-1.3) ... Setting up libkeyutils1:amd64 (1.5.9-9.3) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autopoint (0.19.8.1-9) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.45.0-1) ... Setting up libk5crypto3:amd64 (1.16.1-1ubuntu1) ... Setting up libwind0-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up gettext (0.19.8.1-9) ... Setting up libasn1-8-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libhcrypto4-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.34-2) ... Setting up libhx509-5-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.4-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libkrb5-3:amd64 (1.16.1-1ubuntu1) ... Setting up libkrb5-26-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libheimntlm0-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libtool (2.4.6-6) ... Setting up po-debconf (1.0.21) ... Setting up libgssapi-krb5-2:amd64 (1.16.1-1ubuntu1) ... Setting up libgssapi3-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libldap-2.4-2:amd64 (2.4.46+dfsg-5ubuntu3) ... Setting up libcurl3-gnutls:amd64 (7.61.0-1ubuntu2.2) ... Setting up libcurl4-gnutls-dev:amd64 (7.61.0-1ubuntu2.2) ... Setting up dh-strip-nondeterminism (0.45.0-1) ... Setting up debhelper (11.5.3ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up dh-exec (0.23build1) ... Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-140-generic amd64 (x86_64) Toolchain package versions: binutils_2.31.1-10ubuntu1 dpkg-dev_1.19.2ubuntu1 g++-8_8.2.0-10ubuntu1 gcc-8_8.2.0-10ubuntu1 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-10ubuntu1 libstdc++6_8.2.0-10ubuntu1 linux-libc-dev_4.19.0-7.8 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.8.0~alpha2ubuntu1 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_4.4.18-2ubuntu3 binutils_2.31.1-10ubuntu1 binutils-common_2.31.1-10ubuntu1 binutils-x86-64-linux-gnu_2.31.1-10ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20180409 coreutils_8.28-1ubuntu2 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-10ubuntu1 dash_0.5.10.2-1 debconf_1.5.69 debhelper_11.5.3ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-exec_0.23build1 dh-strip-nondeterminism_0.45.0-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu4 dpkg_1.19.2ubuntu1 dpkg-dev_1.19.2ubuntu1 dwz_0.12-2 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 fakeroot_1.23-1 fdisk_2.32-0.1ubuntu2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-10ubuntu1 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-10ubuntu1 gcc-8-base_8.2.0-10ubuntu1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpg_2.2.8-3ubuntu1 gpg-agent_2.2.8-3ubuntu1 gpgconf_2.2.8-3ubuntu1 gpgv_2.2.8-3ubuntu1 grep_3.1-3 groff-base_1.22.3-10 gzip_1.6-5ubuntu2 hostname_3.21 init_1.56 init-system-helpers_1.56 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu10 libapt-pkg5.0_1.8.0~alpha2ubuntu1 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-10ubuntu1 libasn1-8-heimdal_7.5.0+dfsg-2.1 libassuan0_2.5.1-2 libatomic1_8.2.0-10ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libbinutils_2.31.1-10ubuntu1 libblkid1_2.32-0.1ubuntu2 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libbz2-dev_1.0.6-9 libc-bin_2.28-0ubuntu1 libc-dev-bin_2.28-0ubuntu1 libc6_2.28-0ubuntu1 libc6-dev_2.28-0ubuntu1 libcap-ng0_0.7.9-1build1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-10ubuntu1 libcom-err2_1.44.4-2 libcomerr2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2ubuntu2 libcurl3-gnutls_7.61.0-1ubuntu2.2 libcurl4-gnutls-dev_7.61.0-1ubuntu2.2 libdb5.3_5.3.28+dfsg1-0.2 libdebconfclient0_0.244ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.2ubuntu1 libelf1_0.175-1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.32-0.1ubuntu2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_0.45.0-1 libgcc-8-dev_8.2.0-10ubuntu1 libgcc1_1:8.2.0-10ubuntu1 libgcrypt20_1.8.4-3ubuntu1 libgdbm-compat4_1.18.1-2 libgdbm5_1.14.1-6 libgdbm6_1.18.1-2 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.4-2ubuntu2 libgomp1_8.2.0-10ubuntu1 libgpg-error0_1.32-3 libgssapi-krb5-2_1.16.1-1ubuntu1 libgssapi3-heimdal_7.5.0+dfsg-2.1 libhcrypto4-heimdal_7.5.0+dfsg-2.1 libheimbase1-heimdal_7.5.0+dfsg-2.1 libheimntlm0-heimdal_7.5.0+dfsg-2.1 libhogweed4_3.4.1~rc1-1 libhx509-5-heimdal_7.5.0+dfsg-2.1 libicu63_63.1-5 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.6.1-2ubuntu2 libisl19_0.20-2 libitm1_8.2.0-10ubuntu1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.1-1ubuntu1 libkeyutils1_1.5.9-9.3 libkmod2_25-1ubuntu2 libkrb5-26-heimdal_7.5.0+dfsg-2.1 libkrb5-3_1.16.1-1ubuntu1 libkrb5support0_1.16.1-1ubuntu1 libldap-2.4-2_2.4.46+dfsg-5ubuntu3 libldap-common_2.4.46+dfsg-5ubuntu3 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.2.0-10ubuntu1 liblz4-1_1.8.2-1ubuntu1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32-0.1ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libmpx2_8.2.0-10ubuntu1 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.0-1 libnpth0_1.6-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-11 libperl5.26_5.26.2-7 libperl5.28_5.28.1-2 libpipeline1_1.5.0-2 libpng16-16_1.6.34-2 libprocps7_2:3.3.15-2ubuntu1 libpsl5_0.20.2-2 libquadmath0_8.2.0-10ubuntu1 libreadline7_7.0-5 libroken18-heimdal_7.5.0+dfsg-2.1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-1build2 libsemanage1_2.8-1build2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.32-0.1ubuntu2 libsqlite3-0_3.26.0-1 libss2_1.44.4-2 libssl-dev_1.1.1a-1ubuntu2 libssl1.1_1.1.1a-1ubuntu2 libstdc++-8-dev_8.2.0-10ubuntu1 libstdc++6_8.2.0-10ubuntu1 libsystemd0_239-7ubuntu15 libtasn1-6_4.13-3 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-6 libtsan0_8.2.0-10ubuntu1 libubsan1_8.2.0-10ubuntu1 libudev1_239-7ubuntu15 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu2 libwind0-heimdal_7.5.0+dfsg-2.1 libxml2_2.9.4+dfsg1-7ubuntu3 libzstd1_1.3.5+dfsg-1ubuntu1 linux-libc-dev_4.19.0-7.8 lockfile-progs_0.1.18 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.4-3 mawk_1.3.3-17ubuntu3 mount_2.32-0.1ubuntu2 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1a-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.28.1-2 perl-base_5.28.1-2 perl-modules-5.26_5.26.2-7 perl-modules-5.28_5.28.1-2 pinentry-curses_1.1.0-1build2 pkgbinarymangler_143 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-7ubuntu15 systemd-sysv_239-7ubuntu15 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-3 tzdata_2018g-1 ubuntu-keyring_2018.09.18.1 util-linux_2.32-0.1ubuntu2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Dec 6 06:59:58 2018 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./htslib_1.9-6.dsc dpkg-source: info: extracting htslib in htslib-1.9 dpkg-source: info: unpacking htslib_1.9.orig.tar.gz dpkg-source: info: unpacking htslib_1.9-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying define_PATH_MAX.patch dpkg-source: info: applying fPIC.patch dpkg-source: info: applying testShebang.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-15744970 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15744970 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15744970 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package htslib dpkg-buildpackage: info: source version 1.9-6 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from htslib-1.9/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$ fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make V=1 -j4 distclean make[2]: Entering directory '/<>' rm -f test/*.tmp test/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL* rm -f libhts.so libhts.so.* rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h rm -f libhts.a bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/sam test/test_bgzf test/test_realn test/test-regidx test/test_view test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/test-bcf-translate test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 rm -f config.cache config.h config.log config.mk config.status rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk rm -rf autom4te.cache make[2]: Leaving directory '/<>' rm -rf test_backup/ make[1]: Leaving directory '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/libhts2.substvars debian/libhts-dev.substvars debian/libhts-private-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files rm -fr -- debian/libhts2/ debian/tmp/ debian/libhts-dev/ debian/libhts-private-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 build dh build 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 '/<>' # create clean copy of test dir cp -a test test_backup autoconf dh_auto_configure -- --enable-libcurl ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking shared library type for unknown-Linux... plain .so checking how to run the C preprocessor... gcc -E checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking make[1]: Leaving directory '/<>' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts-private-dev.debhelper.log debian/libhts2.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \ # re-try later LDLIBS=-lhts \ PACKAGE_VERSION="1.9-6" \ libdir=/usr/lib/x86_64-linux-gnu make V=1 -j4 "CFLAGS=-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto" make[2]: Entering directory '/<>' gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9"' > version.h gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_libcurl.o hfile_libcurl.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_gcs.o hfile_gcs.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_s3.o hfile_s3.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o knetfile.pico knetfile.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_net.pico hfile_net.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/files.pico cram/files.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/sam_header.pico cram/sam_header.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c gcc -shared -Wl,-soname,libhts.so.2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm -lcurl -lcrypto ln -sf libhts.so libhts.so.2 ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o ranlib libhts.a gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test make V=1 -j4 test VERBOSE=1 make[1]: Entering directory '/<>' test/hts_endian test/fieldarith test/fieldarith.sam test/hfile test/test_bgzf test/bgziptest.txt 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 Expected passes: 13 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx.fa test/fastqs.fq test/test-regidx cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -t auxf.fa -S -l0 -C -o VERSION=3.0 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram ./test_view -t auxf.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram ./test_view auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram ./test_view c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram ./test_view c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram ./test_view c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram ./test_view c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram ./test_view c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram ./test_view c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram ./test_view c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -t c2.fa -S -l0 -C -o VERSION=3.0 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram ./test_view -t c2.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram ./test_view c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram ./test_view ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam ./test_view ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam ./test_view ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.cram > ce#1000.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram ./test_view ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram ./test_view ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram ./test_view ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram ./test_view ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram ./test_view ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram ./test_view ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram ./test_view ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram ./test_view ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram ./test_view ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram ./test_view ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram ./test_view ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=2.1 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam ./test_view md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -t md.fa -S -l0 -C -o VERSION=3.0 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam ./test_view md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -t md.fa -C -o VERSION=2.1 md#1.tmp.cram > md#1.tmp.cram.cram ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.cram.cram > md#1.tmp.cram ./test_view -t md.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram ./test_view md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram ./test_view xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram ./test_view xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram ./test_view xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram ./test_view xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram ./test_view xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram ./test_view xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram ./test_view xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram ./test_view xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram ./test_view xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram ./test_view xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram ./test_view xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ .. ok ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out test_view testing auxf#values.sam, ref auxf.fa: ./test_view -@4 -S -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view -@4 auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -S -l0 -C -o VERSION=3.0 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view -@4 auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram ./test_view -@4 auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -@4 -S -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view -@4 c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view -@4 c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram ./test_view -@4 c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view -@4 c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view -@4 c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram ./test_view -@4 c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view -@4 c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view -@4 c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram ./test_view -@4 c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view -@4 c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view -@4 c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram ./test_view -@4 c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view -@4 c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view -@4 c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram ./test_view -@4 c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view -@4 c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view -@4 c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram ./test_view -@4 c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -@4 -S -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view -@4 c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view -@4 c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram ./test_view -@4 c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view -@4 c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c2.fa -S -l0 -C -o VERSION=3.0 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view -@4 c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram ./test_view -@4 -t c2.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram ./test_view -@4 c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view -@4 ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view -@4 ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram ./test_view -@4 ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam ./test_view -@4 ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam ./test_view -@4 ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.cram > ce#1000.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram ./test_view -@4 ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view -@4 ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view -@4 ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram ./test_view -@4 ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view -@4 ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view -@4 ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram ./test_view -@4 ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -@4 -S -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view -@4 ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view -@4 ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram ./test_view -@4 ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -@4 -S -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view -@4 ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view -@4 ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram ./test_view -@4 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -@4 -S -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view -@4 ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view -@4 ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram ./test_view -@4 ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -@4 -S -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view -@4 ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view -@4 ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram ./test_view -@4 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view -@4 ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view -@4 ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram ./test_view -@4 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view -@4 ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view -@4 ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram ./test_view -@4 ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view -@4 ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view -@4 ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram ./test_view -@4 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view -@4 ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view -@4 ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram ./test_view -@4 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=2.1 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam ./test_view -@4 md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t md.fa -S -l0 -C -o VERSION=3.0 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam ./test_view -@4 md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t md.fa -C -o VERSION=2.1 md#1.tmp.cram > md#1.tmp.cram.cram ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.cram.cram > md#1.tmp.cram ./test_view -@4 -t md.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram ./test_view -@4 md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view -@4 xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view -@4 xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram ./test_view -@4 xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -@4 -S -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view -@4 xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view -@4 xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram ./test_view -@4 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -@4 -S -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view -@4 xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view -@4 xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram ./test_view -@4 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view -@4 xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view -@4 xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram ./test_view -@4 xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view -@4 xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view -@4 xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram ./test_view -@4 xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -@4 -S -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view -@4 xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view -@4 xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram ./test_view -@4 xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view -@4 xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view -@4 xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram ./test_view -@4 xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view -@4 xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view -@4 xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram ./test_view -@4 xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -@4 -S -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view -@4 xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view -@4 xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram ./test_view -@4 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view -@4 xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view -@4 xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram ./test_view -@4 xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view -@4 xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view -@4 xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram ./test_view -@4 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ .. ok ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out test_vcf_api: /<>/test/test-vcf-api /tmp/0jfJFkXzHT/test-vcf-api.bcf .. ok test_vcf_sweep: /<>/test/test-vcf-sweep /tmp/0jfJFkXzHT/test-vcf-api.bcf .. ok test_vcf_various: /<>/htsfile -ch /<>/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /<>/htsfile -c /<>/test/formatcols.vcf .. ok test_vcf_various: /<>/htsfile -c /<>/test/noroundtrip.vcf .. ok test_vcf_various: /<>/htsfile -c /<>/test/formatmissing.vcf .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/0jfJFkXzHT -s 1485234406 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/0jfJFkXzHT -s 644326469 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/0jfJFkXzHT -s 1484970873 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/0jfJFkXzHT -s 1446859377 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/0jfJFkXzHT -s 562988533 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/0jfJFkXzHT -s 684463621 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/0jfJFkXzHT -s 1537631454 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/0jfJFkXzHT -s 175781217 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/0jfJFkXzHT -s 1281440858 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/0jfJFkXzHT -s 1381915825 .. ok test_command: /<>/test/test-bcf-translate - .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/0jfJFkXzHT/headernul0.bam .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/0jfJFkXzHT/headernul1.bam .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/0jfJFkXzHT/headernul678.bam .. ok test_rebgzip: /<>/bgzip -I /<>/test/bgziptest.txt.gz.gzi -c -g /<>/test/bgziptest.txt .. ok test-logging: /<>/test/test-logging.pl .. ok test_realn: /<>/test/test_realn -f /<>/test/realn01.fa -i /<>/test/realn01.sam -o - .. ok test_realn: /<>/test/test_realn -f /<>/test/realn02.fa -i /<>/test/realn02.sam -o - .. ok test_realn: /<>/test/test_realn -a -f /<>/test/realn01.fa -i /<>/test/realn01.sam -o - .. ok test_realn: /<>/test/test_realn -a -f /<>/test/realn02.fa -i /<>/test/realn02.sam -o - .. ok test_realn: /<>/test/test_realn -e -f /<>/test/realn01.fa -i /<>/test/realn01.sam -o - .. ok test_realn: /<>/test/test_realn -e -f /<>/test/realn02.fa -i /<>/test/realn02.sam -o - .. ok test_realn: /<>/test/test_realn -r -f /<>/test/realn02.fa -i /<>/test/realn02-r.sam -o - .. ok test_realn: /<>/test/test_realn -a -f /<>/test/realn02.fa -i /<>/test/realn02_exp.sam -o - .. ok test_realn: /<>/test/test_realn -f /<>/test/realn02.fa -i /<>/test/realn02_exp-a.sam -o - .. ok Number of tests: total .. 97 passed .. 97 failed .. 0 make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep rm -f -- debian/libhts2.substvars debian/libhts-dev.substvars debian/libhts-private-dev.substvars debian/htslib-test.substvars debian/tabix.substvars rm -fr -- debian/.debhelper/generated/libhts2/ debian/libhts2/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/libhts-private-dev/ debian/libhts-private-dev/ debian/.debhelper/generated/htslib-test/ debian/htslib-test/ debian/.debhelper/generated/tabix/ debian/tabix/ rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts-private-dev.debhelper.log debian/libhts2.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/<>' for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \ rm /<>/test/${binary} ; \ done dh_auto_install -- \ prefix=/usr \ libdir=/usr/lib/x86_64-linux-gnu \ PACKAGE_VERSION="1.9-6" install -d /<>/debian/tmp make V=1 -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr libdir=/usr/lib/x86_64-linux-gnu PACKAGE_VERSION=1.9-6 make[2]: Entering directory '/<>' echo '#define HTS_VERSION "1.9-6"' > version.h mkdir -p -m 755 /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/include /<>/debian/tmp/usr/include/htslib /<>/debian/tmp/usr/lib/x86_64-linux-gnu /<>/debian/tmp/usr/share/man/man1 /<>/debian/tmp/usr/share/man/man5 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c if test -n ""; then mkdir -p -m 755 /<>/debian/tmp; fi gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/x86_64-linux-gnu#g;s#@-PACKAGE_VERSION@#1.9-6#g' htslib.pc.tmp > /<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc chmod 644 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o gcc -shared -Wl,-soname,libhts.so.2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread ranlib libhts.a gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread ln -sf libhts.so libhts.so.2 install -p -m 644 libhts.so /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.9-6 ln -sf libhts.so.1.9-6 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so ln -sf libhts.so.1.9-6 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.2 install -p bgzip htsfile tabix /<>/debian/tmp/usr/bin if test -n ""; then install -p /<>/debian/tmp; fi install -p -m 644 htslib/*.h /<>/debian/tmp/usr/include/htslib install -p -m 644 libhts.a /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a install -p -m 644 bgzip.1 htsfile.1 tabix.1 /<>/debian/tmp/usr/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /<>/debian/tmp/usr/share/man/man5 make[2]: Leaving directory '/<>' # 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 '/<>' dh_install install -d debian/libhts2/usr/lib/x86_64-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.9-6 debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.2 debian/libhts2/usr/lib/x86_64-linux-gnu/ install -d debian/.debhelper/generated/libhts2 install -d debian/libhts-dev/usr/include cp --reflink=auto -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/ install -d debian/libhts-dev/usr/lib/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 -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 -d debian/libhts-dev/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/libhts-dev/usr/share/man/man5/ install -d debian/.debhelper/generated/libhts-dev install -d debian/libhts-private-dev/usr/include/htslib/cram cp --reflink=auto -a ./cram/cram.h ./cram/cram_codecs.h ./cram/cram_decode.h ./cram/cram_encode.h ./cram/cram_index.h ./cram/cram_io.h ./cram/cram_samtools.h ./cram/cram_stats.h ./cram/cram_structs.h ./cram/mFILE.h ./cram/misc.h ./cram/open_trace_file.h ./cram/os.h ./cram/pooled_alloc.h ./cram/rANS_byte.h ./cram/rANS_static.h ./cram/sam_header.h ./cram/string_alloc.h debian/libhts-private-dev/usr/include/htslib/cram/ install -d debian/.debhelper/generated/libhts-private-dev install -d debian/htslib-test/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/tests/run-unit-test debian/htslib-test/usr/share/doc/libhts-dev/ install -d debian/htslib-test/usr/share/htslib-test cp --reflink=auto -a ./Makefile ./bcf_sr_sort.c ./bcf_sr_sort.h ./bgzf.c ./bgzip.c ./config.h ./config.mk ./errmod.c ./faidx.c ./hfile.c ./hfile_gcs.c ./hfile_internal.h ./hfile_libcurl.c ./hfile_net.c ./hfile_s3.c ./hts.c ./hts_internal.h ./hts_os.c ./htsfile.c ./htslib.mk ./htslib_vars.mk ./kfunc.c ./knetfile.c ./kstring.c ./md5.c ./multipart.c ./os ./plugin.c ./probaln.c ./realn.c ./regidx.c ./sam.c ./synced_bcf_reader.c ./tabix.c ./tbx.c ./textutils.c ./textutils_internal.h ./thread_pool.c ./thread_pool_internal.h ./vcf.c ./vcf_sweep.c ./vcfutils.c ./version.h ./version.sh debian/htslib-test/usr/share/htslib-test/ install -d debian/htslib-test/usr/share/htslib-test/cram cp --reflink=auto -a ./cram/cram.h ./cram/cram_codecs.c ./cram/cram_codecs.h ./cram/cram_decode.c ./cram/cram_decode.h ./cram/cram_encode.c ./cram/cram_encode.h ./cram/cram_external.c ./cram/cram_index.c ./cram/cram_index.h ./cram/cram_io.c ./cram/cram_io.h ./cram/cram_samtools.c ./cram/cram_samtools.h ./cram/cram_stats.c ./cram/cram_stats.h ./cram/cram_structs.h ./cram/files.c ./cram/mFILE.c ./cram/mFILE.h ./cram/misc.h ./cram/open_trace_file.c ./cram/open_trace_file.h ./cram/os.h ./cram/pooled_alloc.c ./cram/pooled_alloc.h ./cram/rANS_byte.h ./cram/rANS_static.c ./cram/rANS_static.h ./cram/sam_header.c ./cram/sam_header.h ./cram/string_alloc.c ./cram/string_alloc.h debian/htslib-test/usr/share/htslib-test/cram/ install -d debian/htslib-test/usr/share/htslib-test/test cp --reflink=auto -a ./test/auxf\#values.sam ./test/auxf\#values_java.cram ./test/auxf.fa ./test/auxf.fa.fai ./test/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/compare_sam.pl ./test/cross_validate.sh ./test/faidx.fa ./test/fastqs.fq ./test/fastqs_README.txt ./test/fieldarith.c ./test/fieldarith.sam ./test/formatcols.vcf ./test/formatmissing-out.vcf ./test/formatmissing.vcf ./test/hfile.c ./test/hts_endian.c ./test/md\#1.sam ./test/md.fa ./test/md.fa.fai ./test/noroundtrip-out.vcf ./test/noroundtrip.vcf ./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/tabix ./test/test-bcf-sr.c ./test/test-bcf-sr.pl ./test/test-bcf-translate.c ./test/test-bcf-translate.out ./test/test-logging.pl ./test/test-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_realn.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/thread_pool.md ./test/xx\#blank.sam ./test/xx\#large_aux.sam ./test/xx\#large_aux2.sam ./test/xx\#large_aux_java.cram ./test/xx\#minimal.sam ./test/xx\#pair.sam ./test/xx\#repeated.sam ./test/xx\#rg.sam ./test/xx\#tlen.sam ./test/xx\#tlen2.sam ./test/xx\#triplet.sam ./test/xx\#unsorted.sam ./test/xx.fa ./test/xx.fa.fai debian/htslib-test/usr/share/htslib-test/test/ install -d debian/.debhelper/generated/htslib-test install -d debian/tabix/usr/bin cp --reflink=auto -a ./bgzip ./htsfile ./tabix debian/tabix/usr/bin/ install -d debian/.debhelper/generated/tabix dh_installdocs install -d debian/libhts2/usr/share/doc/libhts2 install -p -m0644 debian/copyright debian/libhts2/usr/share/doc/libhts2/copyright install -d debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/README.test debian/libhts-dev/usr/share/doc/libhts-dev chown -R 0:0 debian/libhts-dev/usr/share/doc chmod -R u\+rw,go=rX debian/libhts-dev/usr/share/doc install -p -m0644 debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright install -d debian/libhts-private-dev/usr/share/doc/libhts-private-dev install -p -m0644 debian/copyright debian/libhts-private-dev/usr/share/doc/libhts-private-dev/copyright install -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/copyright debian/htslib-test/usr/share/doc/htslib-test/copyright install -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts-private-dev.debhelper.log debian/libhts2.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs NEWS install -p -m0644 debian/changelog debian/tabix/usr/share/doc/tabix/changelog.Debian install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog install -p -m0644 debian/changelog debian/libhts-private-dev/usr/share/doc/libhts-private-dev/changelog.Debian install -p -m0644 NEWS debian/libhts-private-dev/usr/share/doc/libhts-private-dev/changelog install -p -m0644 debian/changelog debian/htslib-test/usr/share/doc/htslib-test/changelog.Debian install -p -m0644 NEWS debian/htslib-test/usr/share/doc/htslib-test/changelog install -p -m0644 debian/changelog debian/libhts2/usr/share/doc/libhts2/changelog.Debian install -p -m0644 NEWS debian/libhts2/usr/share/doc/libhts2/changelog install -p -m0644 debian/changelog debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog make[1]: Leaving directory '/<>' dh_installman install -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./htsfile.1 debian/tabix/usr/share/man/man1/htsfile.1 install -p -m0644 ./tabix.1 debian/tabix/usr/share/man/man1/tabix.1 man -l --recode UTF-8 ./debian/libhts-dev/usr/share/man/man5/vcf.5 > debian/libhts-dev/usr/share/man/man5/vcf.5.dh-new man -l --recode UTF-8 ./debian/libhts-dev/usr/share/man/man5/faidx.5 > debian/libhts-dev/usr/share/man/man5/faidx.5.dh-new man -l --recode UTF-8 ./debian/tabix/usr/share/man/man1/tabix.1 > debian/tabix/usr/share/man/man1/tabix.1.dh-new mv debian/libhts-dev/usr/share/man/man5/vcf.5.dh-new debian/libhts-dev/usr/share/man/man5/vcf.5 man -l --recode UTF-8 ./debian/libhts-dev/usr/share/man/man5/sam.5 > debian/libhts-dev/usr/share/man/man5/sam.5.dh-new mv debian/libhts-dev/usr/share/man/man5/faidx.5.dh-new debian/libhts-dev/usr/share/man/man5/faidx.5 man -l --recode UTF-8 ./debian/tabix/usr/share/man/man1/htsfile.1 > debian/tabix/usr/share/man/man1/htsfile.1.dh-new mv debian/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1 chmod 0644 -- debian/tabix/usr/share/man/man1/tabix.1 mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1 chmod 0644 -- debian/libhts-dev/usr/share/man/man5/faidx.5 debian/tabix/usr/share/man/man1/htsfile.1 mv debian/libhts-dev/usr/share/man/man5/sam.5.dh-new debian/libhts-dev/usr/share/man/man5/sam.5 chmod 0644 -- debian/libhts-dev/usr/share/man/man5/vcf.5 debian/libhts-dev/usr/share/man/man5/sam.5 dh_perl (grep -a -s -v perl:Depends debian/htslib-test.substvars; echo perl:Depends=perl:any) > debian/htslib-test.substvars.new mv debian/htslib-test.substvars.new debian/htslib-test.substvars dh_link rm -f debian/libhts2/usr/lib/x86_64-linux-gnu/libhts.so.2 ln -s libhts.so.1.9-6 debian/libhts2/usr/lib/x86_64-linux-gnu/libhts.so.2 rm -f debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so ln -s libhts.so.1.9-6 debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz ln -s tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz dh_strip_nondeterminism Using 1544079563 as canonical time Normalizing debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.a using File::StripNondeterminism::handlers::ar Using 1544079563 as canonical time Normalizing debian/htslib-test/usr/share/htslib-test/test/bgziptest.txt.gz using File::StripNondeterminism::handlers::gzip dh_compress cd debian/libhts2 cd debian/libhts-private-dev cd debian/tabix chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 chmod a-x usr/share/doc/libhts-private-dev/changelog usr/share/doc/libhts-private-dev/changelog.Debian cd '/<>' chmod a-x usr/share/doc/libhts2/changelog usr/share/doc/libhts2/changelog.Debian gzip -9nf usr/share/doc/libhts2/changelog usr/share/doc/libhts2/changelog.Debian cd '/<>' cd debian/libhts-dev gzip -9nf usr/share/doc/libhts-private-dev/changelog usr/share/doc/libhts-private-dev/changelog.Debian cd '/<>' cd debian/htslib-test chmod a-x usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 gzip -9nf usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 cd '/<>' chmod a-x usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian gzip -9nf usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian cd '/<>' dh_fixperms find debian/libhts2 -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/libhts-private-dev -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/tabix -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/libhts2 ! -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/libhts-private-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts2/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts2/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-private-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts-private-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts2/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/libhts2 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-private-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts2/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libhts-private-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/libhts-private-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/htslib-test -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 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/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts-dev/usr/share/man debian/libhts-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 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/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/htslib-test/usr/share/doc -type f -a -true -a ! -regex 'debian/htslib-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/htslib-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing dh_strip install -d debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/0c objcopy --only-keep-debug --compress-debug-sections debian/libhts2/usr/lib/x86_64-linux-gnu/libhts.so.1.9-6 debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/0c/4540f0f6ae19a543f4ecc75f74236e85e7a491.debug install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/b8 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/b8/a9d3c4158f7577dc2d2340ba1f4f40fbd6a03b.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/b8/a9d3c4158f7577dc2d2340ba1f4f40fbd6a03b.debug chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/b8/a9d3c4158f7577dc2d2340ba1f4f40fbd6a03b.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/b8/a9d3c4158f7577dc2d2340ba1f4f40fbd6a03b.debug debian/tabix/usr/bin/htsfile chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/0c/4540f0f6ae19a543f4ecc75f74236e85e7a491.debug chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/0c/4540f0f6ae19a543f4ecc75f74236e85e7a491.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts2/usr/lib/x86_64-linux-gnu/libhts.so.1.9-6 objcopy --add-gnu-debuglink debian/.debhelper/libhts2/dbgsym-root/usr/lib/debug/.build-id/0c/4540f0f6ae19a543f4ecc75f74236e85e7a491.debug debian/libhts2/usr/lib/x86_64-linux-gnu/libhts.so.1.9-6 install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/1a objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/1a/52df7e6578d11f05e463d3d42465220e361620.debug install -d debian/.debhelper/libhts2/dbgsym-root/usr/share/doc ln -s libhts2 debian/.debhelper/libhts2/dbgsym-root/usr/share/doc/libhts2-dbgsym strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.a chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/1a/52df7e6578d11f05e463d3d42465220e361620.debug chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/1a/52df7e6578d11f05e463d3d42465220e361620.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/1a/52df7e6578d11f05e463d3d42465220e361620.debug debian/tabix/usr/bin/tabix install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c5 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c5/b224e2f10f62417ea233b862cf6e40df759f75.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c5/b224e2f10f62417ea233b862cf6e40df759f75.debug chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/c5/b224e2f10f62417ea233b862cf6e40df759f75.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/c5/b224e2f10f62417ea233b862cf6e40df759f75.debug debian/tabix/usr/bin/bgzip install -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym dh_makeshlibs rm -f debian/libhts2/DEBIAN/shlibs install -d debian/libhts2/DEBIAN echo "libhts 2 libhts2" >> debian/libhts2/DEBIAN/shlibs chmod 0644 -- debian/libhts2/DEBIAN/shlibs chown 0:0 -- debian/libhts2/DEBIAN/shlibs dpkg-gensymbols -plibhts2 -Idebian/libhts2.symbols -Pdebian/libhts2 -edebian/libhts2/usr/lib/x86_64-linux-gnu/libhts.so.1.9-6 mv debian/.debhelper/generated/libhts2/triggers.new debian/.debhelper/generated/libhts2/triggers rm -f debian/libhts-dev/DEBIAN/shlibs rm -f debian/libhts-private-dev/DEBIAN/shlibs rm -f debian/htslib-test/DEBIAN/shlibs rm -f debian/tabix/DEBIAN/shlibs dh_shlibdeps dpkg-shlibdeps -Tdebian/libhts2.substvars debian/libhts2/usr/lib/x86_64-linux-gnu/libhts.so.1.9-6 install -d debian/tabix/DEBIAN dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix debian/tabix/usr/bin/bgzip dh_installdeb install -p -m0644 debian/.debhelper/generated/libhts2/triggers debian/libhts2/DEBIAN/triggers install -d debian/libhts-dev/DEBIAN install -d debian/libhts-private-dev/DEBIAN install -d debian/htslib-test/DEBIAN dh_gencontrol echo misc:Depends= >> debian/libhts-private-dev.substvars echo misc:Pre-Depends= >> debian/libhts-private-dev.substvars dpkg-gencontrol -plibhts-private-dev -ldebian/changelog -Tdebian/libhts-private-dev.substvars -Pdebian/libhts-private-dev echo misc:Depends= >> debian/libhts2.substvars echo misc:Pre-Depends= >> debian/libhts2.substvars install -d debian/.debhelper/libhts2/dbgsym-root/DEBIAN dpkg-gencontrol -plibhts2 -ldebian/changelog -Tdebian/libhts2.substvars -Pdebian/.debhelper/libhts2/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=libhts2-dbgsym "-DDepends=libhts2 (= \${binary:Version})" "-DDescription=debug symbols for libhts2" -DBuild-Ids=0c4540f0f6ae19a543f4ecc75f74236e85e7a491 -DSection=debug -DPackage-Type=ddeb -UReplaces -UBreaks echo misc:Depends= >> debian/tabix.substvars echo misc:Pre-Depends= >> debian/tabix.substvars install -d debian/.debhelper/tabix/dbgsym-root/DEBIAN dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/.debhelper/tabix/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=1a52df7e6578d11f05e463d3d42465220e361620 b8a9d3c4158f7577dc2d2340ba1f4f40fbd6a03b c5b224e2f10f62417ea233b862cf6e40df759f75" -DSection=debug -DPackage-Type=ddeb -UReplaces -UBreaks chmod 0644 -- debian/libhts-private-dev/DEBIAN/control chown 0:0 -- debian/libhts-private-dev/DEBIAN/control 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/.debhelper/libhts2/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibhts2 -ldebian/changelog -Tdebian/libhts2.substvars -Pdebian/libhts2 chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix chmod 0644 -- debian/tabix/DEBIAN/control chown 0:0 -- debian/tabix/DEBIAN/control chmod 0644 -- debian/htslib-test/DEBIAN/control chown 0:0 -- debian/htslib-test/DEBIAN/control chmod 0644 -- debian/libhts2/DEBIAN/control chown 0:0 -- debian/libhts2/DEBIAN/control echo misc:Depends= >> debian/libhts-dev.substvars echo misc:Pre-Depends= >> debian/libhts-dev.substvars dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -Pdebian/libhts-dev chmod 0644 -- debian/libhts-dev/DEBIAN/control chown 0:0 -- debian/libhts-dev/DEBIAN/control dh_md5sums cd debian/libhts2 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libhts-private-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts-private-dev/DEBIAN/md5sums chown 0:0 -- debian/libhts-private-dev/DEBIAN/md5sums chmod 0644 -- debian/tabix/DEBIAN/md5sums chown 0:0 -- debian/tabix/DEBIAN/md5sums cd debian/.debhelper/tabix/dbgsym-root >/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/libhts2/DEBIAN/md5sums chown 0:0 -- debian/libhts2/DEBIAN/md5sums cd debian/.debhelper/libhts2/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/libhts2/dbgsym-root/DEBIAN/md5sums cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums chown 0:0 -- debian/libhts-dev/DEBIAN/md5sums chmod 0644 -- debian/htslib-test/DEBIAN/md5sums chown 0:0 -- debian/htslib-test/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/libhts2 .. dpkg-deb --build debian/libhts-dev .. dpkg-deb --build debian/htslib-test .. install -d debian/.debhelper/scratch-space/build-tabix dpkg-deb --build debian/.debhelper/tabix/dbgsym-root debian/.debhelper/scratch-space/build-tabix INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 pkgstriptranslations: processing htslib-test (in debian/htslib-test); do_strip: , oemstrip: pkgstriptranslations: processing tabix-dbgsym (in debian/.debhelper/tabix/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing libhts-dev (in debian/libhts-dev); do_strip: , oemstrip: pkgstriptranslations: processing libhts2 (in debian/libhts2); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/htslib-test/DEBIAN/control, package htslib-test, directory debian/htslib-test .. removing usr/share/doc/htslib-test/changelog.gz pkgstripfiles: processing control file: debian/libhts-dev/DEBIAN/control, package libhts-dev, directory debian/libhts-dev pkgstripfiles: processing control file: debian/.debhelper/tabix/dbgsym-root/DEBIAN/control, package tabix-dbgsym, directory debian/.debhelper/tabix/dbgsym-root dpkg-deb: building package 'tabix-dbgsym' in 'debian/.debhelper/scratch-space/build-tabix/tabix-dbgsym_1.9-6_amd64.deb'. INFO: pkgstripfiles: waiting for lock (htslib-test) ... .. removing usr/share/doc/libhts-dev/changelog.gz INFO: pkgstripfiles: waiting for lock (libhts-dev) ... pkgstripfiles: processing control file: debian/libhts2/DEBIAN/control, package libhts2, directory debian/libhts2 .. removing usr/share/doc/libhts2/changelog.gz pkgstripfiles: Truncating usr/share/doc/libhts2/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package libhts2 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libhts2' in '../libhts2_1.9-6_amd64.deb'. install -d debian/.debhelper/scratch-space/build-libhts2 dpkg-deb --build debian/.debhelper/libhts2/dbgsym-root debian/.debhelper/scratch-space/build-libhts2 INFO: pkgstripfiles: waiting for lock (htslib-test) ... INFO: pkgstriptranslations version 143 Searching for duplicated docs in dependency libhts2... symlinking changelog.Debian.gz in libhts-dev to file in libhts2 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libhts-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.9-6_amd64.deb'. Renaming tabix-dbgsym_1.9-6_amd64.deb to tabix-dbgsym_1.9-6_amd64.ddeb mv debian/.debhelper/scratch-space/build-tabix/tabix-dbgsym_1.9-6_amd64.deb ../tabix-dbgsym_1.9-6_amd64.ddeb pkgstriptranslations: processing libhts2-dbgsym (in debian/.debhelper/libhts2/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/libhts2/dbgsym-root/DEBIAN/control, package libhts2-dbgsym, directory debian/.debhelper/libhts2/dbgsym-root dpkg-deb: building package 'libhts2-dbgsym' in 'debian/.debhelper/scratch-space/build-libhts2/libhts2-dbgsym_1.9-6_amd64.deb'. dpkg-deb --build debian/libhts-private-dev .. INFO: pkgstripfiles: waiting for lock (htslib-test) ... Renaming libhts2-dbgsym_1.9-6_amd64.deb to libhts2-dbgsym_1.9-6_amd64.ddeb mv debian/.debhelper/scratch-space/build-libhts2/libhts2-dbgsym_1.9-6_amd64.deb ../libhts2-dbgsym_1.9-6_amd64.ddeb INFO: pkgstriptranslations version 143 pkgstriptranslations: processing libhts-private-dev (in debian/libhts-private-dev); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libhts-private-dev/DEBIAN/control, package libhts-private-dev, directory debian/libhts-private-dev .. removing usr/share/doc/libhts-private-dev/changelog.gz Searching for duplicated docs in dependency libhts-dev... symlinking changelog.Debian.gz in libhts-private-dev to file in libhts2 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libhts-private-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libhts-private-dev' in '../libhts-private-dev_1.9-6_all.deb'. Searching for duplicated docs in dependency libhts-private-dev... symlinking changelog.Debian.gz in htslib-test to file in libhts2 pkgstripfiles: Running PNG optimization (using 4 cpus) for package htslib-test ... pkgstripfiles: No PNG files. dpkg-deb: building package 'htslib-test' in '../htslib-test_1.9-6_all.deb'. dpkg-deb --build debian/tabix .. INFO: pkgstriptranslations version 143 pkgstriptranslations: processing tabix (in debian/tabix); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/tabix/DEBIAN/control, package tabix, directory debian/tabix .. removing usr/share/doc/tabix/changelog.gz pkgstripfiles: Truncating usr/share/doc/tabix/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package tabix ... pkgstripfiles: No PNG files. dpkg-deb: building package 'tabix' in '../tabix_1.9-6_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../htslib_1.9-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from htslib-1.9/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20181206-1111 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ htslib_1.9-6_amd64.changes: --------------------------- Format: 1.8 Date: Wed, 05 Dec 2018 22:59:23 -0800 Source: htslib Binary: libhts2 libhts-dev libhts-private-dev htslib-test tabix Architecture: all amd64 Version: 1.9-6 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Michael R. Crusoe Description: htslib-test - Test data for HTSlib libhts-dev - development files for the HTSlib libhts-private-dev - private development files for the HTSlib (use with care) libhts2 - C library for high-throughput sequencing data formats tabix - generic indexer for TAB-delimited genome position files Changes: htslib (1.9-6) unstable; urgency=medium . * Revert libdeflate for DEFLATE based (de)compression and its crc32 implementation. Checksums-Sha1: 8f5f7f32ee3bdc290b067ec07439c89fa127454f 903996 htslib-test_1.9-6_all.deb 39fd59fcf40f4c355db0a6f15538df528f08396f 7436 htslib_1.9-6_amd64.buildinfo d0048741ae8e89ec8dad59c483ffc9c543125dfa 389884 libhts-dev_1.9-6_amd64.deb e40218b4acce4e888821da7217c4e6e7de2fe5a9 29352 libhts-private-dev_1.9-6_all.deb 77419268ca8fd6870865f3668a0c6c27acfe627d 1015620 libhts2-dbgsym_1.9-6_amd64.ddeb d4d9ff60a805501029c0080553e3a7c18e57d5ee 305632 libhts2_1.9-6_amd64.deb 2d3861819183ccb1ebc33fdf64d5b0ba616cf1de 2556184 tabix-dbgsym_1.9-6_amd64.ddeb 965ee8a53e914ab10530bd9722a9a9718603d22e 334892 tabix_1.9-6_amd64.deb Checksums-Sha256: 2a285282726b3c44c67c1d4543b9d105b791d48db19b04262e5e6177deb815f1 903996 htslib-test_1.9-6_all.deb ff8ea97bba4e062a2295ba0c20e8ddfa9b7b5e579935444f2da36bc5d5b8b18f 7436 htslib_1.9-6_amd64.buildinfo 7e9b500bb4589906ac42dc2c8867abcbf4d818be7107a53deae52d808a817f67 389884 libhts-dev_1.9-6_amd64.deb 67e3ac6fcc2c8705f58ec0afc3168e6fc170f7d79ba83c2fc37634dfb1f3299e 29352 libhts-private-dev_1.9-6_all.deb 2f6b8562c2f6083a70037b30f5975e3736b39911218db55f3c7dcaba7d7efab5 1015620 libhts2-dbgsym_1.9-6_amd64.ddeb 1fb0fb82695edd2c15d6358ed2f4f31f5b67017d1463d19cad31c0db058badb7 305632 libhts2_1.9-6_amd64.deb 0ba94ba9e4a3b034f30bca5e7d22139627e96a10bc54881848ff4e4e71d4d68a 2556184 tabix-dbgsym_1.9-6_amd64.ddeb fd0978790d1e0ceef9b6c8ae5e3d24ff679385f6c405629af964b97dc5f10057 334892 tabix_1.9-6_amd64.deb Files: d89898bb4019884eb7137d5ca000529d 903996 science optional htslib-test_1.9-6_all.deb a853a13e4481693baae46df5b92ae78e 7436 science optional htslib_1.9-6_amd64.buildinfo 57bb818c47bbb9cd57469f8d5cfa37f6 389884 libdevel optional libhts-dev_1.9-6_amd64.deb 2453ea6b8bc40de4c542b0c2c212cabb 29352 libdevel optional libhts-private-dev_1.9-6_all.deb 11a561c75f9532b064880251be6444ac 1015620 debug optional libhts2-dbgsym_1.9-6_amd64.ddeb f638076ac095ffbf319b19549c41adb3 305632 libs optional libhts2_1.9-6_amd64.deb 8d16cfb4074394812c1a1c5fec22b029 2556184 debug optional tabix-dbgsym_1.9-6_amd64.ddeb 4de6cf101ba49aba6f5e18bbfda679e9 334892 science optional tabix_1.9-6_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ htslib-test_1.9-6_all.deb ------------------------- new debian package, version 2.0. size 903996 bytes: control archive=5732 bytes. 1038 bytes, 23 lines control 14567 bytes, 198 lines md5sums Package: htslib-test Source: htslib Version: 1.9-6 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 6403 Depends: libhts-private-dev, perl:any Section: science Priority: optional Homepage: https://github.com/samtools/htslib Description: Test data for HTSlib HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package contains test files and scripts for the HTSlib. drwxr-xr-x root/root 0 2018-12-06 06:59 ./ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/doc/htslib-test/ lrwxrwxrwx root/root 0 2018-12-06 06:59 ./usr/share/doc/htslib-test/changelog.Debian.gz -> ../libhts2/changelog.Debian.gz -rw-r--r-- root/root 5762 2018-10-14 16:54 ./usr/share/doc/htslib-test/copyright drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/doc/libhts-dev/ -rw-r--r-- root/root 386 2018-10-14 16:54 ./usr/share/doc/libhts-dev/run-unit-test drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/htslib-test/ -rw-r--r-- root/root 23394 2018-12-06 06:59 ./usr/share/htslib-test/Makefile -rw-r--r-- root/root 21895 2018-07-18 08:33 ./usr/share/htslib-test/bcf_sr_sort.c -rw-r--r-- root/root 3857 2018-07-18 08:33 ./usr/share/htslib-test/bcf_sr_sort.h -rw-r--r-- root/root 63908 2018-07-18 08:33 ./usr/share/htslib-test/bgzf.c -rw-r--r-- root/root 13927 2018-07-18 08:33 ./usr/share/htslib-test/bgzip.c -rw-r--r-- root/root 4124 2018-12-06 06:59 ./usr/share/htslib-test/config.h -rw-r--r-- root/root 3523 2018-12-06 06:59 ./usr/share/htslib-test/config.mk drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/htslib-test/cram/ -rw-r--r-- root/root 2412 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram.h -rw-r--r-- root/root 56940 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_codecs.c -rw-r--r-- root/root 6439 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_codecs.h -rw-r--r-- root/root 120328 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_decode.c -rw-r--r-- root/root 3687 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_decode.h -rw-r--r-- root/root 111424 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_encode.c -rw-r--r-- root/root 3626 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_encode.h -rw-r--r-- root/root 13347 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_external.c -rw-r--r-- root/root 18858 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_index.c -rw-r--r-- root/root 3427 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_index.h -rw-r--r-- root/root 132236 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_io.c -rw-r--r-- root/root 27866 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_io.h -rw-r--r-- root/root 5583 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_samtools.c -rw-r--r-- root/root 3758 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_samtools.h -rw-r--r-- root/root 6007 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_stats.c -rw-r--r-- root/root 2272 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_stats.h -rw-r--r-- root/root 24264 2018-07-18 08:33 ./usr/share/htslib-test/cram/cram_structs.h -rw-r--r-- root/root 2457 2018-07-18 08:33 ./usr/share/htslib-test/cram/files.c -rw-r--r-- root/root 16807 2018-07-18 08:33 ./usr/share/htslib-test/cram/mFILE.c -rw-r--r-- 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./usr/share/htslib-test/hts_internal.h -rw-r--r-- root/root 1723 2018-07-18 08:33 ./usr/share/htslib-test/hts_os.c -rw-r--r-- root/root 8007 2018-07-18 08:33 ./usr/share/htslib-test/htsfile.c -rw-r--r-- root/root 5817 2018-07-18 08:33 ./usr/share/htslib-test/htslib.mk -rw-r--r-- root/root 2931 2018-07-18 08:33 ./usr/share/htslib-test/htslib_vars.mk -rw-r--r-- root/root 9166 2018-07-18 08:33 ./usr/share/htslib-test/kfunc.c -rw-r--r-- root/root 19072 2018-07-18 08:33 ./usr/share/htslib-test/knetfile.c -rw-r--r-- root/root 9317 2018-07-18 08:33 ./usr/share/htslib-test/kstring.c -rw-r--r-- root/root 10579 2018-07-18 08:33 ./usr/share/htslib-test/md5.c -rw-r--r-- root/root 8406 2018-07-18 08:33 ./usr/share/htslib-test/multipart.c drwxr-xr-x root/root 0 2018-07-18 08:33 ./usr/share/htslib-test/os/ -rw-r--r-- root/root 2345 2018-07-18 08:33 ./usr/share/htslib-test/os/lzma_stub.h -rw-r--r-- root/root 2648 2018-07-18 08:33 ./usr/share/htslib-test/os/rand.c -rw-r--r-- root/root 5566 2018-07-18 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libhts-dev Source: htslib Version: 1.9-6 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1431 Depends: libhts2 (= 1.9-6), liblzma-dev, zlib1g-dev Section: libdevel Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: development files for the HTSlib HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package contains development files for the HTSlib: headers, static library, manual pages, etc. drwxr-xr-x root/root 0 2018-12-06 06:59 ./ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/include/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/include/htslib/ -rw-r--r-- root/root 14797 2018-07-18 08:33 ./usr/include/htslib/bgzf.h -rw-r--r-- root/root 15393 2018-07-18 08:33 ./usr/include/htslib/cram.h -rw-r--r-- root/root 8972 2018-07-18 08:33 ./usr/include/htslib/faidx.h -rw-r--r-- root/root 10077 2018-07-18 08:33 ./usr/include/htslib/hfile.h -rw-r--r-- root/root 30459 2018-07-18 08:33 ./usr/include/htslib/hts.h -rw-r--r-- root/root 3336 2018-07-18 08:33 ./usr/include/htslib/hts_defs.h -rw-r--r-- root/root 11446 2018-07-18 08:33 ./usr/include/htslib/hts_endian.h -rw-r--r-- root/root 3898 2018-07-18 08:33 ./usr/include/htslib/hts_log.h -rw-r--r-- root/root 1996 2018-07-18 08:33 ./usr/include/htslib/hts_os.h -rw-r--r-- root/root 4195 2018-07-18 08:33 ./usr/include/htslib/kbitset.h -rw-r--r-- root/root 2716 2018-07-18 08:33 ./usr/include/htslib/kfunc.h -rw-r--r-- root/root 21540 2018-07-18 08:33 ./usr/include/htslib/khash.h -rw-r--r-- root/root 3990 2018-07-18 08:33 ./usr/include/htslib/khash_str2int.h -rw-r--r-- root/root 5086 2018-07-18 08:33 ./usr/include/htslib/klist.h -rw-r--r-- root/root 2850 2018-07-18 08:33 ./usr/include/htslib/knetfile.h -rw-r--r-- root/root 9139 2018-07-18 08:33 ./usr/include/htslib/kseq.h -rw-r--r-- root/root 10567 2018-07-18 08:33 ./usr/include/htslib/ksort.h -rw-r--r-- root/root 7012 2018-07-18 08:33 ./usr/include/htslib/kstring.h -rw-r--r-- root/root 5834 2018-07-18 08:33 ./usr/include/htslib/regidx.h -rw-r--r-- root/root 29580 2018-07-18 08:33 ./usr/include/htslib/sam.h -rw-r--r-- root/root 14954 2018-07-18 08:33 ./usr/include/htslib/synced_bcf_reader.h -rw-r--r-- root/root 3118 2018-07-18 08:33 ./usr/include/htslib/tbx.h -rw-r--r-- root/root 9386 2018-07-18 08:33 ./usr/include/htslib/thread_pool.h -rw-r--r-- root/root 43671 2018-07-18 08:33 ./usr/include/htslib/vcf.h -rw-r--r-- root/root 1602 2018-07-18 08:33 ./usr/include/htslib/vcf_sweep.h -rw-r--r-- root/root 4819 2018-07-18 08:33 ./usr/include/htslib/vcfutils.h drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/lib/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 1130582 2018-12-06 06:59 ./usr/lib/x86_64-linux-gnu/libhts.a lrwxrwxrwx root/root 0 2018-12-06 06:59 ./usr/lib/x86_64-linux-gnu/libhts.so -> libhts.so.1.9-6 drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/lib/x86_64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 612 2018-12-06 06:59 ./usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/doc/libhts-dev/ -rw-r--r-- root/root 401 2018-10-14 16:54 ./usr/share/doc/libhts-dev/README.test lrwxrwxrwx root/root 0 2018-12-06 06:59 ./usr/share/doc/libhts-dev/changelog.Debian.gz -> ../libhts2/changelog.Debian.gz -rw-r--r-- root/root 5762 2018-10-14 16:54 ./usr/share/doc/libhts-dev/copyright drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/man/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/man/man5/ -rw-r--r-- root/root 2452 2018-12-06 06:59 ./usr/share/man/man5/faidx.5.gz -rw-r--r-- root/root 1535 2018-12-06 06:59 ./usr/share/man/man5/sam.5.gz -rw-r--r-- root/root 1854 2018-12-06 06:59 ./usr/share/man/man5/vcf.5.gz libhts-private-dev_1.9-6_all.deb -------------------------------- new debian package, version 2.0. size 29352 bytes: control archive=1488 bytes. 1177 bytes, 25 lines control 1344 bytes, 19 lines md5sums Package: libhts-private-dev Source: htslib Version: 1.9-6 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 165 Depends: libhts-dev (>= 1.5-5) Breaks: libhts-dev (<= 1.5-4) Section: libdevel Priority: optional Homepage: https://github.com/samtools/htslib Description: private development files for the HTSlib (use with care) HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package contains private header files for the HTSlib. They are *not* intended for general use but libseqlib needs these files. drwxr-xr-x root/root 0 2018-12-06 06:59 ./ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/include/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/include/htslib/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/include/htslib/cram/ -rw-r--r-- root/root 2412 2018-07-18 08:33 ./usr/include/htslib/cram/cram.h -rw-r--r-- root/root 6439 2018-07-18 08:33 ./usr/include/htslib/cram/cram_codecs.h -rw-r--r-- root/root 3687 2018-07-18 08:33 ./usr/include/htslib/cram/cram_decode.h -rw-r--r-- root/root 3626 2018-07-18 08:33 ./usr/include/htslib/cram/cram_encode.h -rw-r--r-- root/root 3427 2018-07-18 08:33 ./usr/include/htslib/cram/cram_index.h -rw-r--r-- root/root 27866 2018-07-18 08:33 ./usr/include/htslib/cram/cram_io.h -rw-r--r-- root/root 3758 2018-07-18 08:33 ./usr/include/htslib/cram/cram_samtools.h -rw-r--r-- root/root 2272 2018-07-18 08:33 ./usr/include/htslib/cram/cram_stats.h -rw-r--r-- root/root 24264 2018-07-18 08:33 ./usr/include/htslib/cram/cram_structs.h -rw-r--r-- root/root 3054 2018-07-18 08:33 ./usr/include/htslib/cram/mFILE.h -rw-r--r-- root/root 4283 2018-07-18 08:33 ./usr/include/htslib/cram/misc.h -rw-r--r-- root/root 5002 2018-07-18 08:33 ./usr/include/htslib/cram/open_trace_file.h -rw-r--r-- root/root 7262 2018-12-06 06:59 ./usr/include/htslib/cram/os.h -rw-r--r-- root/root 2177 2018-07-18 08:33 ./usr/include/htslib/cram/pooled_alloc.h -rw-r--r-- root/root 12297 2018-07-18 08:33 ./usr/include/htslib/cram/rANS_byte.h -rw-r--r-- root/root 2075 2018-07-18 08:33 ./usr/include/htslib/cram/rANS_static.h -rw-r--r-- root/root 14139 2018-07-18 08:33 ./usr/include/htslib/cram/sam_header.h -rw-r--r-- root/root 2312 2018-07-18 08:33 ./usr/include/htslib/cram/string_alloc.h drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/doc/libhts-private-dev/ lrwxrwxrwx root/root 0 2018-12-06 06:59 ./usr/share/doc/libhts-private-dev/changelog.Debian.gz -> ../libhts2/changelog.Debian.gz -rw-r--r-- root/root 5762 2018-10-14 16:54 ./usr/share/doc/libhts-private-dev/copyright libhts2_1.9-6_amd64.deb ----------------------- new debian package, version 2.0. size 305632 bytes: control archive=4804 bytes. 1181 bytes, 23 lines control 217 bytes, 3 lines md5sums 17 bytes, 1 lines shlibs 20119 bytes, 747 lines symbols 74 bytes, 2 lines triggers Package: libhts2 Source: htslib Version: 1.9-6 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 755 Depends: libbz2-1.0, libc6 (>= 2.23), libcurl3-gnutls (>= 7.18.0), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.2.0) Breaks: python-pysam (<< 0.15~), python3-pysam (<< 0.15~) Section: libs Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: C library for high-throughput sequencing data formats HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. drwxr-xr-x root/root 0 2018-12-06 06:59 ./ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/lib/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 722888 2018-12-06 06:59 ./usr/lib/x86_64-linux-gnu/libhts.so.1.9-6 lrwxrwxrwx root/root 0 2018-12-06 06:59 ./usr/lib/x86_64-linux-gnu/libhts.so.2 -> libhts.so.1.9-6 drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/doc/libhts2/ -rw-r--r-- root/root 1098 2018-12-06 06:59 ./usr/share/doc/libhts2/changelog.Debian.gz -rw-r--r-- root/root 5762 2018-10-14 16:54 ./usr/share/doc/libhts2/copyright tabix_1.9-6_amd64.deb --------------------- new debian package, version 2.0. size 334892 bytes: control archive=1108 bytes. 1021 bytes, 20 lines control 414 bytes, 7 lines md5sums Package: tabix Source: htslib Version: 1.9-6 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1754 Depends: libbz2-1.0, libc6 (>= 2.15), libcurl3-gnutls (>= 7.18.0), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.2.0) Section: science Priority: optional Homepage: https://github.com/samtools/htslib Description: generic indexer for TAB-delimited genome position files Tabix indexes files where some columns indicate sequence coordinates: name (usually a chromosome), start and stop. The input data file must be position sorted and compressed by bgzip (provided in this package), which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines by chromosomal coordinates. Fast data retrieval also works over network if an URI is given as a file name. . This version of tabix is built from the HTSlib source. drwxr-xr-x root/root 0 2018-12-06 06:59 ./ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/bin/ -rwxr-xr-x root/root 526416 2018-12-06 06:59 ./usr/bin/bgzip -rwxr-xr-x root/root 608368 2018-12-06 06:59 ./usr/bin/htsfile -rwxr-xr-x root/root 624752 2018-12-06 06:59 ./usr/bin/tabix drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/doc/tabix/ -rw-r--r-- root/root 1098 2018-12-06 06:59 ./usr/share/doc/tabix/changelog.Debian.gz -rw-r--r-- root/root 5762 2018-10-14 16:54 ./usr/share/doc/tabix/copyright drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/man/ drwxr-xr-x root/root 0 2018-12-06 06:59 ./usr/share/man/man1/ lrwxrwxrwx root/root 0 2018-12-06 06:59 ./usr/share/man/man1/bgzip.1.gz -> tabix.1.gz -rw-r--r-- root/root 1700 2018-12-06 06:59 ./usr/share/man/man1/htsfile.1.gz -rw-r--r-- root/root 2770 2018-12-06 06:59 ./usr/share/man/man1/tabix.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 86444 Build-Time: 117 Distribution: disco-proposed Host Architecture: amd64 Install-Time: 14 Job: htslib_1.9-6.dsc Machine Architecture: amd64 Package: htslib Package-Time: 132 Source-Version: 1.9-6 Space: 86444 Status: successful Version: 1.9-6 -------------------------------------------------------------------------------- Finished at 20181206-1111 Build needed 00:02:12, 86444k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15744970 Scanning for processes to kill in build PACKAGEBUILD-15744970