https://launchpad.net/ubuntu/+source/htslib/1.10.2-2ubuntu2/+build/18704120 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-ppc64el-011 4.4.0-173-generic #203-Ubuntu SMP Wed Jan 15 02:55:15 UTC 2020 ppc64le Buildd toolchain package versions: launchpad-buildd_186 python-lpbuildd_186 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_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 13 Feb 19:35:51 ntpdate[1876]: adjust time server 10.211.37.1 offset 0.075296 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=ppc64el PACKAGEBUILD-18704120 --image-type chroot /home/buildd/filecache-default/dc614fa4772464ee6d43f8f857199c7f024663c7 Creating target for build PACKAGEBUILD-18704120 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=ppc64el PACKAGEBUILD-18704120 Starting target for build PACKAGEBUILD-18704120 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=ppc64el PACKAGEBUILD-18704120 'deb http://ftpmaster.internal/ubuntu focal main universe' 'deb http://ftpmaster.internal/ubuntu focal-security main universe' 'deb http://ftpmaster.internal/ubuntu focal-updates main universe' 'deb http://ftpmaster.internal/ubuntu focal-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-18704120 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=ppc64el PACKAGEBUILD-18704120 Updating target for build PACKAGEBUILD-18704120 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal-security InRelease [79.7 kB] Get:3 http://ftpmaster.internal/ubuntu focal-updates InRelease [79.7 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed InRelease [255 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main ppc64el Packages [962 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main Translation-en [506 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe ppc64el Packages [8406 kB] Get:8 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5151 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el Packages [77.8 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [40.7 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/universe ppc64el Packages [346 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [242 kB] Fetched 16.4 MB in 4s (4561 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: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: gcc-10-base libctf-nobfd0 libctf0 libffi7 libgcc-s1 libhogweed5 libisl22 libnettle7 libperl5.30 perl-modules-5.30 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-common binutils-powerpc64le-linux-gnu bsdutils bzip2 cpp-9 debianutils e2fsprogs fdisk g++-9 gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv grep gzip hostname libacl1 libapparmor1 libapt-pkg5.90 libasan5 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcryptsetup12 libdebconfclient0 libdevmapper1.02.1 libext2fs2 libfdisk1 libgcc-9-dev libgcc1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libitm1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblsan0 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpng16-16 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login logsave lsb-base mount ncurses-base ncurses-bin openssl passwd perl perl-base sensible-utils systemd systemd-sysv sysvinit-utils ubuntu-keyring util-linux 109 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 66.8 MB of archives. After this operation, 52.6 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main ppc64el libc6-dev ppc64el 2.30-0ubuntu3 [2556 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main ppc64el libc-dev-bin ppc64el 2.30-0ubuntu3 [72.8 kB] Get:3 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el linux-libc-dev ppc64el 5.4.0-14.17 [1128 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main ppc64el gcc-10-base ppc64el 10-20200211-1ubuntu1 [18.8 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main ppc64el libgcc-s1 ppc64el 10-20200211-1ubuntu1 [30.3 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main ppc64el libgcc1 ppc64el 1:10-20200211-1ubuntu1 [30.2 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main ppc64el libc6 ppc64el 2.30-0ubuntu3 [2700 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main ppc64el base-files ppc64el 11ubuntu2 [60.3 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main ppc64el debianutils ppc64el 4.9.1 [86.6 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main ppc64el bash ppc64el 5.0-5ubuntu1 [716 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el bsdutils ppc64el 1:2.34-0.1ubuntu6 [67.6 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main ppc64el grep ppc64el 3.4-1 [155 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main ppc64el gzip ppc64el 1.10-0ubuntu4 [104 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main ppc64el hostname ppc64el 3.23 [11.8 kB] Get:15 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el login ppc64el 1:4.8.1-1ubuntu1 [224 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main ppc64el ncurses-bin ppc64el 6.1+20191019-1ubuntu1 [179 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main ppc64el perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main ppc64el libperl5.30 ppc64el 5.30.0-9 [3914 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main ppc64el perl ppc64el 5.30.0-9 [224 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main ppc64el perl-base ppc64el 5.30.0-9 [1494 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main ppc64el bzip2 ppc64el 1.0.8-2 [36.9 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main ppc64el libbz2-1.0 ppc64el 1.0.8-2 [43.3 kB] Get:23 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libblkid1 ppc64el 2.34-0.1ubuntu6 [158 kB] Get:24 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libuuid1 ppc64el 2.34-0.1ubuntu6 [21.7 kB] Get:25 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libfdisk1 ppc64el 2.34-0.1ubuntu6 [193 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main ppc64el libpcre2-8-0 ppc64el 10.34-7 [203 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main ppc64el libselinux1 ppc64el 3.0-1 [81.1 kB] Get:28 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libmount1 ppc64el 2.34-0.1ubuntu6 [170 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main ppc64el libncurses6 ppc64el 6.1+20191019-1ubuntu1 [120 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main ppc64el libtinfo6 ppc64el 6.1+20191019-1ubuntu1 [101 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main ppc64el libncursesw6 ppc64el 6.1+20191019-1ubuntu1 [152 kB] Get:32 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libsmartcols1 ppc64el 2.34-0.1ubuntu6 [112 kB] Get:33 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el fdisk ppc64el 2.34-0.1ubuntu6 [128 kB] Get:34 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el util-linux ppc64el 2.34-0.1ubuntu6 [1066 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main ppc64el libdebconfclient0 ppc64el 0.251ubuntu1 [6088 B] Get:36 http://ftpmaster.internal/ubuntu focal/main ppc64el base-passwd ppc64el 3.5.47 [50.2 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main ppc64el libc-bin ppc64el 2.30-0ubuntu3 [626 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main ppc64el ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main ppc64el lsb-base all 11.1.0ubuntu2 [12.1 kB] Get:40 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el sysvinit-utils ppc64el 2.96-2.1ubuntu1 [22.8 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main ppc64el libgpg-error0 ppc64el 1.36-7ubuntu1 [69.1 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main ppc64el libgcrypt20 ppc64el 1.8.5-3ubuntu1 [439 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main ppc64el liblz4-1 ppc64el 1.9.2-2 [62.0 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main ppc64el libstdc++6 ppc64el 10-20200211-1ubuntu1 [547 kB] Get:45 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el systemd-sysv ppc64el 244.2-1ubuntu1 [9368 B] Get:46 http://ftpmaster.internal/ubuntu focal/main ppc64el libacl1 ppc64el 2.2.53-5ubuntu1 [20.3 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main ppc64el libapparmor1 ppc64el 2.13.3-7ubuntu1 [38.0 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main ppc64el libaudit-common all 1:2.8.5-2ubuntu5 [4076 B] Get:49 http://ftpmaster.internal/ubuntu focal/main ppc64el libcap-ng0 ppc64el 0.7.9-2.1build1 [11.7 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main ppc64el libaudit1 ppc64el 1:2.8.5-2ubuntu5 [42.7 kB] Get:51 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libcap2 ppc64el 1:2.31-1 [17.2 kB] Get:52 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libudev1 ppc64el 244.2-1ubuntu1 [89.7 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.155-2ubuntu8 [153 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main ppc64el libjson-c4 ppc64el 0.13.1+dfsg-6 [33.1 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main ppc64el libssl1.1 ppc64el 1.1.1d-2ubuntu3 [1359 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main ppc64el libcryptsetup12 ppc64el 2:2.2.2-3ubuntu1 [213 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main ppc64el libnettle7 ppc64el 3.5.1+really3.5.1-2 [145 kB] Get:58 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libgmp10 ppc64el 2:6.2.0+dfsg-3 [235 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main ppc64el libhogweed5 ppc64el 3.5.1+really3.5.1-2 [140 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main ppc64el libffi7 ppc64el 3.3-3 [21.8 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main ppc64el libp11-kit0 ppc64el 0.23.20-1build1 [201 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main ppc64el libtasn1-6 ppc64el 4.15.0-2 [44.7 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main ppc64el libgnutls30 ppc64el 3.6.11.1-2ubuntu2 [774 kB] Get:64 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libkmod2 ppc64el 26+20191223-1ubuntu1 [51.7 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main ppc64el libpam0g ppc64el 1.3.1-5ubuntu4 [60.8 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main ppc64el libseccomp2 ppc64el 2.4.2-2ubuntu2 [48.8 kB] Get:67 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el mount ppc64el 2.34-0.1ubuntu6 [122 kB] Get:68 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el systemd ppc64el 244.2-1ubuntu1 [4411 kB] Get:69 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libsystemd0 ppc64el 244.2-1ubuntu1 [301 kB] Get:70 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libzstd1 ppc64el 1.4.4+dfsg-3 [298 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main ppc64el libapt-pkg5.90 ppc64el 1.9.9 [918 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main ppc64el gpgv ppc64el 2.2.17-3ubuntu1 [232 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main ppc64el ubuntu-keyring all 2020.02.11.1 [22.3 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main ppc64el apt ppc64el 1.9.9 [1310 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main ppc64el libpam-modules-bin ppc64el 1.3.1-5ubuntu4 [42.5 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main ppc64el libpam-modules ppc64el 1.3.1-5ubuntu4 [282 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main ppc64el logsave ppc64el 1.45.3-4ubuntu3 [10.3 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main ppc64el libext2fs2 ppc64el 1.45.3-4ubuntu3 [211 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main ppc64el e2fsprogs ppc64el 1.45.3-4ubuntu3 [552 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main ppc64el libattr1 ppc64el 1:2.4.48-5 [13.6 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main ppc64el libpam-runtime all 1.3.1-5ubuntu4 [37.3 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main ppc64el libsepol1 ppc64el 3.0-1 [284 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main ppc64el libsemanage-common all 3.0-1 [9880 B] Get:84 http://ftpmaster.internal/ubuntu focal/main ppc64el libsemanage1 ppc64el 3.0-1 [95.5 kB] Get:85 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el passwd ppc64el 1:4.8.1-1ubuntu1 [805 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main ppc64el libgomp1 ppc64el 10-20200211-1ubuntu1 [107 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main ppc64el libitm1 ppc64el 10-20200211-1ubuntu1 [28.6 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main ppc64el libatomic1 ppc64el 10-20200211-1ubuntu1 [9836 B] Get:89 http://ftpmaster.internal/ubuntu focal/main ppc64el libasan5 ppc64el 9.2.1-28ubuntu1 [408 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main ppc64el liblsan0 ppc64el 10-20200211-1ubuntu1 [157 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main ppc64el libtsan0 ppc64el 10-20200211-1ubuntu1 [326 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main ppc64el libubsan1 ppc64el 10-20200211-1ubuntu1 [149 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main ppc64el libquadmath0 ppc64el 10-20200211-1ubuntu1 [153 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main ppc64el g++-9 ppc64el 9.2.1-28ubuntu1 [7742 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main ppc64el gcc-9 ppc64el 9.2.1-28ubuntu1 [7539 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main ppc64el libstdc++-9-dev ppc64el 9.2.1-28ubuntu1 [1749 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main ppc64el libgcc-9-dev ppc64el 9.2.1-28ubuntu1 [1259 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main ppc64el libisl22 ppc64el 0.22-2 [691 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main ppc64el libcc1-0 ppc64el 10-20200211-1ubuntu1 [41.6 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.34-1ubuntu1 [1748 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main ppc64el libbinutils ppc64el 2.34-1ubuntu1 [513 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main ppc64el binutils ppc64el 2.34-1ubuntu1 [3376 B] Get:103 http://ftpmaster.internal/ubuntu focal/main ppc64el binutils-common ppc64el 2.34-1ubuntu1 [206 kB] Get:104 http://ftpmaster.internal/ubuntu focal/main ppc64el libctf-nobfd0 ppc64el 2.34-1ubuntu1 [52.9 kB] Get:105 http://ftpmaster.internal/ubuntu focal/main ppc64el libctf0 ppc64el 2.34-1ubuntu1 [52.8 kB] Get:106 http://ftpmaster.internal/ubuntu focal/main ppc64el cpp-9 ppc64el 9.2.1-28ubuntu1 [6831 kB] Get:107 http://ftpmaster.internal/ubuntu focal/main ppc64el gcc-9-base ppc64el 9.2.1-28ubuntu1 [19.1 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main ppc64el libcom-err2 ppc64el 1.45.3-4ubuntu3 [9580 B] Get:109 http://ftpmaster.internal/ubuntu focal/main ppc64el libss2 ppc64el 1.45.3-4ubuntu3 [12.4 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main ppc64el sensible-utils all 0.0.12+nmu1 [15.0 kB] Get:111 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libsqlite3-0 ppc64el 3.31.1-1ubuntu1 [577 kB] Get:112 http://ftpmaster.internal/ubuntu focal/main ppc64el openssl ppc64el 1.1.1d-2ubuntu3 [618 kB] Get:113 http://ftpmaster.internal/ubuntu focal/main ppc64el libpng16-16 ppc64el 1.6.37-2 [208 kB] Get:114 http://ftpmaster.internal/ubuntu focal/main ppc64el libassuan0 ppc64el 2.5.3-7ubuntu2 [38.3 kB] Get:115 http://ftpmaster.internal/ubuntu focal/main ppc64el gpg ppc64el 2.2.17-3ubuntu1 [532 kB] Get:116 http://ftpmaster.internal/ubuntu focal/main ppc64el gpgconf ppc64el 2.2.17-3ubuntu1 [144 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main ppc64el gpg-agent ppc64el 2.2.17-3ubuntu1 [267 kB] Get:118 http://ftpmaster.internal/ubuntu focal/main ppc64el liblockfile-bin ppc64el 1.16-1.1 [12.1 kB] Get:119 http://ftpmaster.internal/ubuntu focal/main ppc64el liblockfile1 ppc64el 1.16-1.1 [7236 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 66.8 MB in 1s (68.0 MB/s) (Reading database ... 12684 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.30-0ubuntu3_ppc64el.deb ... Unpacking libc6-dev:ppc64el (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../libc-dev-bin_2.30-0ubuntu3_ppc64el.deb ... Unpacking libc-dev-bin (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../linux-libc-dev_5.4.0-14.17_ppc64el.deb ... Unpacking linux-libc-dev:ppc64el (5.4.0-14.17) over (5.3.0-18.19) ... Selecting previously unselected package gcc-10-base:ppc64el. Preparing to unpack .../gcc-10-base_10-20200211-1ubuntu1_ppc64el.deb ... Unpacking gcc-10-base:ppc64el (10-20200211-1ubuntu1) ... Setting up gcc-10-base:ppc64el (10-20200211-1ubuntu1) ... Selecting previously unselected package libgcc-s1:ppc64el. (Reading database ... 12694 files and directories currently installed.) Preparing to unpack .../libgcc-s1_10-20200211-1ubuntu1_ppc64el.deb ... Unpacking libgcc-s1:ppc64el (10-20200211-1ubuntu1) ... Replacing files in old package libgcc1:ppc64el (1:9.2.1-9ubuntu2) ... Setting up libgcc-s1:ppc64el (10-20200211-1ubuntu1) ... (Reading database ... 12696 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a10-20200211-1ubuntu1_ppc64el.deb ... Unpacking libgcc1 (1:10-20200211-1ubuntu1) over (1:9.2.1-9ubuntu2) ... Setting up libgcc1 (1:10-20200211-1ubuntu1) ... (Reading database ... 12697 files and directories currently installed.) Preparing to unpack .../libc6_2.30-0ubuntu3_ppc64el.deb ... Unpacking libc6:ppc64el (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Setting up libc6:ppc64el (2.30-0ubuntu3) ... (Reading database ... 12697 files and directories currently installed.) Preparing to unpack .../base-files_11ubuntu2_ppc64el.deb ... Unpacking base-files (11ubuntu2) over (10.2ubuntu7) ... Setting up base-files (11ubuntu2) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... 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Setting up binutils-common:ppc64el (2.34-1ubuntu1) ... Setting up linux-libc-dev:ppc64el (5.4.0-14.17) ... Setting up libctf-nobfd0:ppc64el (2.34-1ubuntu1) ... Setting up libcom-err2:ppc64el (1.45.3-4ubuntu3) ... Setting up libassuan0:ppc64el (2.5.3-7ubuntu2) ... Setting up libgomp1:ppc64el (10-20200211-1ubuntu1) ... Setting up bzip2 (1.0.8-2) ... Setting up libcap2:ppc64el (1:2.31-1) ... Setting up libncurses6:ppc64el (6.1+20191019-1ubuntu1) ... Setting up libquadmath0:ppc64el (10-20200211-1ubuntu1) ... Setting up libpng16-16:ppc64el (1.6.37-2) ... Setting up libatomic1:ppc64el (10-20200211-1ubuntu1) ... Setting up libss2:ppc64el (1.45.3-4ubuntu3) ... Setting up logsave (1.45.3-4ubuntu3) ... Setting up libubsan1:ppc64el (10-20200211-1ubuntu1) ... Setting up libdevmapper1.02.1:ppc64el (2:1.02.155-2ubuntu8) ... Setting up mount (2.34-0.1ubuntu6) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up gpgconf (2.2.17-3ubuntu1) ... Setting up libperl5.30:ppc64el (5.30.0-9) ... Setting up libisl22:ppc64el (0.22-2) ... Setting up liblockfile1:ppc64el (1.16-1.1) ... Setting up libjson-c4:ppc64el (0.13.1+dfsg-6) ... Setting up libbinutils:ppc64el (2.34-1ubuntu1) ... Setting up libc-dev-bin (2.30-0ubuntu3) ... Setting up openssl (1.1.1d-2ubuntu3) ... Setting up libcc1-0:ppc64el (10-20200211-1ubuntu1) ... Setting up gpg (2.2.17-3ubuntu1) ... Setting up liblsan0:ppc64el (10-20200211-1ubuntu1) ... Setting up libitm1:ppc64el (10-20200211-1ubuntu1) ... Setting up libkmod2:ppc64el (26+20191223-1ubuntu1) ... Setting up gcc-9-base:ppc64el (9.2.1-28ubuntu1) ... Setting up libtsan0:ppc64el (10-20200211-1ubuntu1) ... Setting up libctf0:ppc64el (2.34-1ubuntu1) ... Setting up gpg-agent (2.2.17-3ubuntu1) ... Installing new version of config file /etc/logcheck/ignore.d.server/gpg-agent ... Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket -> /usr/lib/systemd/user/gpg-agent-browser.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket -> /usr/lib/systemd/user/gpg-agent-extra.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket -> /usr/lib/systemd/user/gpg-agent-ssh.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent.socket -> /usr/lib/systemd/user/gpg-agent.socket. Setting up e2fsprogs (1.45.3-4ubuntu3) ... Setting up libasan5:ppc64el (9.2.1-28ubuntu1) ... Setting up perl (5.30.0-9) ... Setting up cpp-9 (9.2.1-28ubuntu1) ... Setting up libc6-dev:ppc64el (2.30-0ubuntu3) ... Setting up libcryptsetup12:ppc64el (2:2.2.2-3ubuntu1) ... Setting up binutils-powerpc64le-linux-gnu (2.34-1ubuntu1) ... Setting up systemd (244.2-1ubuntu1) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up binutils (2.34-1ubuntu1) ... Setting up libgcc-9-dev:ppc64el (9.2.1-28ubuntu1) ... Setting up gcc-9 (9.2.1-28ubuntu1) ... Setting up systemd-sysv (244.2-1ubuntu1) ... Setting up libstdc++-9-dev:ppc64el (9.2.1-28ubuntu1) ... Setting up g++-9 (9.2.1-28ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18704120 ppc64el focal-proposed -c chroot:build-PACKAGEBUILD-18704120 --arch=ppc64el --dist=focal-proposed --nolog htslib_1.10.2-2ubuntu2.dsc Initiating build PACKAGEBUILD-18704120 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-173-generic #203-Ubuntu SMP Wed Jan 15 02:55:15 UTC 2020 ppc64le sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-ppc64el-011.buildd +==============================================================================+ | htslib 1.10.2-2ubuntu2 (ppc64el) 13 Feb 2020 19:36 | +==============================================================================+ Package: htslib Version: 1.10.2-2ubuntu2 Source Version: 1.10.2-2ubuntu2 Distribution: focal-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el I: NOTICE: Log filtering will replace 'build/htslib-BsPOfS/htslib-1.10.2' with '<>' I: NOTICE: Log filtering will replace 'build/htslib-BsPOfS' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18704120/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- htslib_1.10.2-2ubuntu2.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-58PMb9/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-58PMb9/apt_archive ./ InRelease Get:2 copy:/<>/resolver-58PMb9/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-58PMb9/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-58PMb9/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-58PMb9/apt_archive ./ Packages [529 B] Fetched 2862 B in 0s (164 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: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 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-58PMb9/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 ... 14614 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 12), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev Filtered Build-Depends: debhelper-compat (= 12), dh-exec, libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev dpkg-deb: building package 'sbuild-build-depends-htslib-dummy' in '/<>/resolver-VjQQF0/apt_archive/sbuild-build-depends-htslib-dummy.deb'. Ign:1 copy:/<>/resolver-VjQQF0/apt_archive ./ InRelease Get:2 copy:/<>/resolver-VjQQF0/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-VjQQF0/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-VjQQF0/apt_archive ./ Sources [260 B] Get:5 copy:/<>/resolver-VjQQF0/apt_archive ./ Packages [579 B] Fetched 2958 B in 0s (178 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: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 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 libbrotli1 libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libicu65 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 libssh-4 libssl-dev libsub-override-perl libtool libuchardet0 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 libbrotli1 libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libicu65 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 libssh-4 libssl-dev libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db po-debconf sbuild-build-depends-htslib-dummy zlib1g-dev 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 23.0 MB of archives. After this operation, 97.8 MB of additional disk space will be used. Get:1 copy:/<>/resolver-VjQQF0/apt_archive ./ sbuild-build-depends-htslib-dummy 0.invalid.0 [908 B] Get:2 http://ftpmaster.internal/ubuntu focal/main ppc64el libbsd0 ppc64el 0.10.0-1 [55.1 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main ppc64el bsdmainutils ppc64el 11.1.2ubuntu2 [185 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main ppc64el libuchardet0 ppc64el 0.0.6-3 [67.7 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main ppc64el groff-base ppc64el 1.22.4-4 [941 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main ppc64el libpipeline1 ppc64el 1.5.2-2build1 [28.9 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main ppc64el man-db ppc64el 2.9.0-2 [1145 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main ppc64el libmagic-mgc ppc64el 1:5.38-4 [218 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main ppc64el libmagic1 ppc64el 1:5.38-4 [93.1 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main ppc64el file ppc64el 1:5.38-4 [24.2 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main ppc64el libelf1 ppc64el 0.176-1.1build1 [53.4 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main ppc64el libglib2.0-0 ppc64el 2.63.3-3 [1376 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libicu65 ppc64el 65.1-1ubuntu1 [8577 kB] Get:14 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libxml2 ppc64el 2.9.4+dfsg1-8ubuntu4 [680 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main ppc64el gettext-base ppc64el 0.19.8.1-10 [52.7 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main ppc64el libkrb5support0 ppc64el 1.17-6ubuntu4 [34.9 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main ppc64el libk5crypto3 ppc64el 1.17-6ubuntu4 [102 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main ppc64el libkeyutils1 ppc64el 1.6-6ubuntu1 [11.3 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main ppc64el libkrb5-3 ppc64el 1.17-6ubuntu4 [371 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main ppc64el libgssapi-krb5-2 ppc64el 1.17-6ubuntu4 [135 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main ppc64el libpsl5 ppc64el 0.20.2-2 [52.2 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main ppc64el libsigsegv2 ppc64el 2.12-2 [13.9 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main ppc64el m4 ppc64el 1.4.18-4 [210 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main ppc64el autoconf all 2.69-11.1 [321 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main ppc64el autotools-dev all 20180224.1 [39.6 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main ppc64el automake all 1:1.16.1-4ubuntu6 [522 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main ppc64el autopoint all 0.19.8.1-10 [412 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main ppc64el libtool all 2.4.6-12 [195 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main ppc64el dh-autoreconf all 19 [16.1 kB] Get:30 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libdebhelper-perl all 12.9ubuntu1 [62.0 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main ppc64el libarchive-zip-perl all 1.67-1 [90.4 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main ppc64el libsub-override-perl all 0.09-2 [9532 B] Get:33 http://ftpmaster.internal/ubuntu focal/main ppc64el libfile-stripnondeterminism-perl all 1.6.3-2 [16.0 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main ppc64el dh-strip-nondeterminism all 1.6.3-2 [5228 B] Get:35 http://ftpmaster.internal/ubuntu focal/main ppc64el dwz ppc64el 0.13-5 [136 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main ppc64el libcroco3 ppc64el 0.6.13-1 [92.1 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main ppc64el gettext ppc64el 0.19.8.1-10 [959 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main ppc64el intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main ppc64el po-debconf all 1.0.21 [233 kB] Get:40 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el debhelper all 12.9ubuntu1 [869 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main ppc64el libroken18-heimdal ppc64el 7.7.0+dfsg-1 [46.5 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main ppc64el libasn1-8-heimdal ppc64el 7.7.0+dfsg-1 [176 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main ppc64el libbrotli1 ppc64el 1.0.7-6 [293 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main ppc64el libbz2-dev ppc64el 1.0.8-2 [43.2 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main ppc64el libheimbase1-heimdal ppc64el 7.7.0+dfsg-1 [32.5 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main ppc64el libhcrypto4-heimdal ppc64el 7.7.0+dfsg-1 [108 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main ppc64el libwind0-heimdal ppc64el 7.7.0+dfsg-1 [49.0 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main ppc64el libhx509-5-heimdal ppc64el 7.7.0+dfsg-1 [120 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main ppc64el libkrb5-26-heimdal ppc64el 7.7.0+dfsg-1 [234 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main ppc64el libheimntlm0-heimdal ppc64el 7.7.0+dfsg-1 [17.4 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main ppc64el libgssapi3-heimdal ppc64el 7.7.0+dfsg-1 [105 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main ppc64el libsasl2-modules-db ppc64el 2.1.27+dfsg-2 [16.9 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main ppc64el libsasl2-2 ppc64el 2.1.27+dfsg-2 [60.2 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main ppc64el libldap-common all 2.4.49+dfsg-1ubuntu1 [17.2 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main ppc64el libldap-2.4-2 ppc64el 2.4.49+dfsg-1ubuntu1 [176 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main ppc64el libnghttp2-14 ppc64el 1.40.0-1 [91.7 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build1 [59.3 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main ppc64el libssh-4 ppc64el 0.9.3-2ubuntu1 [195 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main ppc64el libcurl3-gnutls ppc64el 7.66.0-1ubuntu1 [255 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main ppc64el libcurl4-gnutls-dev ppc64el 7.66.0-1ubuntu1 [356 kB] Get:61 http://ftpmaster.internal/ubuntu focal/universe ppc64el libdeflate0 ppc64el 1.5-3 [63.7 kB] Get:62 http://ftpmaster.internal/ubuntu focal/universe ppc64el libdeflate-dev ppc64el 1.5-3 [47.6 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main ppc64el libssl-dev ppc64el 1.1.1d-2ubuntu3 [1666 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main ppc64el zlib1g-dev ppc64el 1:1.2.11.dfsg-1ubuntu3 [176 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main ppc64el dh-exec ppc64el 0.23.2 [26.1 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main ppc64el liblzma-dev ppc64el 5.2.4-1 [166 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 23.0 MB in 1s (29.7 MB/s) Selecting previously unselected package libbsd0:ppc64el. (Reading database ... 14614 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_ppc64el.deb ... Unpacking libbsd0:ppc64el (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu2_ppc64el.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package libuchardet0:ppc64el. Preparing to unpack .../02-libuchardet0_0.0.6-3_ppc64el.deb ... Unpacking libuchardet0:ppc64el (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-4_ppc64el.deb ... Unpacking groff-base (1.22.4-4) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../04-libpipeline1_1.5.2-2build1_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.5.2-2build1) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.9.0-2_ppc64el.deb ... Unpacking man-db (2.9.0-2) ... 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Selecting previously unselected package libxml2:ppc64el. Preparing to unpack .../12-libxml2_2.9.4+dfsg1-8ubuntu4_ppc64el.deb ... Unpacking libxml2:ppc64el (2.9.4+dfsg1-8ubuntu4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../13-gettext-base_0.19.8.1-10_ppc64el.deb ... Unpacking gettext-base (0.19.8.1-10) ... Selecting previously unselected package libkrb5support0:ppc64el. Preparing to unpack .../14-libkrb5support0_1.17-6ubuntu4_ppc64el.deb ... Unpacking libkrb5support0:ppc64el (1.17-6ubuntu4) ... Selecting previously unselected package libk5crypto3:ppc64el. Preparing to unpack .../15-libk5crypto3_1.17-6ubuntu4_ppc64el.deb ... Unpacking libk5crypto3:ppc64el (1.17-6ubuntu4) ... Selecting previously unselected package libkeyutils1:ppc64el. Preparing to unpack .../16-libkeyutils1_1.6-6ubuntu1_ppc64el.deb ... Unpacking libkeyutils1:ppc64el (1.6-6ubuntu1) ... Selecting previously unselected package libkrb5-3:ppc64el. 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Selecting previously unselected package libbrotli1:ppc64el. Preparing to unpack .../41-libbrotli1_1.0.7-6_ppc64el.deb ... Unpacking libbrotli1:ppc64el (1.0.7-6) ... Selecting previously unselected package libbz2-dev:ppc64el. Preparing to unpack .../42-libbz2-dev_1.0.8-2_ppc64el.deb ... Unpacking libbz2-dev:ppc64el (1.0.8-2) ... Selecting previously unselected package libheimbase1-heimdal:ppc64el. Preparing to unpack .../43-libheimbase1-heimdal_7.7.0+dfsg-1_ppc64el.deb ... Unpacking libheimbase1-heimdal:ppc64el (7.7.0+dfsg-1) ... Selecting previously unselected package libhcrypto4-heimdal:ppc64el. Preparing to unpack .../44-libhcrypto4-heimdal_7.7.0+dfsg-1_ppc64el.deb ... Unpacking libhcrypto4-heimdal:ppc64el (7.7.0+dfsg-1) ... Selecting previously unselected package libwind0-heimdal:ppc64el. Preparing to unpack .../45-libwind0-heimdal_7.7.0+dfsg-1_ppc64el.deb ... Unpacking libwind0-heimdal:ppc64el (7.7.0+dfsg-1) ... Selecting previously unselected package libhx509-5-heimdal:ppc64el. 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Preparing to unpack .../56-libssh-4_0.9.3-2ubuntu1_ppc64el.deb ... Unpacking libssh-4:ppc64el (0.9.3-2ubuntu1) ... Selecting previously unselected package libcurl3-gnutls:ppc64el. Preparing to unpack .../57-libcurl3-gnutls_7.66.0-1ubuntu1_ppc64el.deb ... Unpacking libcurl3-gnutls:ppc64el (7.66.0-1ubuntu1) ... Selecting previously unselected package libcurl4-gnutls-dev:ppc64el. Preparing to unpack .../58-libcurl4-gnutls-dev_7.66.0-1ubuntu1_ppc64el.deb ... Unpacking libcurl4-gnutls-dev:ppc64el (7.66.0-1ubuntu1) ... Selecting previously unselected package libdeflate0. Preparing to unpack .../59-libdeflate0_1.5-3_ppc64el.deb ... Unpacking libdeflate0 (1.5-3) ... Selecting previously unselected package libdeflate-dev:ppc64el. Preparing to unpack .../60-libdeflate-dev_1.5-3_ppc64el.deb ... Unpacking libdeflate-dev:ppc64el (1.5-3) ... Selecting previously unselected package libssl-dev:ppc64el. Preparing to unpack .../61-libssl-dev_1.1.1d-2ubuntu3_ppc64el.deb ... Unpacking libssl-dev:ppc64el (1.1.1d-2ubuntu3) ... Selecting previously unselected package zlib1g-dev:ppc64el. Preparing to unpack .../62-zlib1g-dev_1%3a1.2.11.dfsg-1ubuntu3_ppc64el.deb ... Unpacking zlib1g-dev:ppc64el (1:1.2.11.dfsg-1ubuntu3) ... Selecting previously unselected package dh-exec. Preparing to unpack .../63-dh-exec_0.23.2_ppc64el.deb ... Unpacking dh-exec (0.23.2) ... Selecting previously unselected package liblzma-dev:ppc64el. Preparing to unpack .../64-liblzma-dev_5.2.4-1_ppc64el.deb ... Unpacking liblzma-dev:ppc64el (5.2.4-1) ... Selecting previously unselected package sbuild-build-depends-htslib-dummy. Preparing to unpack .../65-sbuild-build-depends-htslib-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-htslib-dummy (0.invalid.0) ... Setting up libpipeline1:ppc64el (1.5.2-2build1) ... Setting up libkeyutils1:ppc64el (1.6-6ubuntu1) ... Setting up libpsl5:ppc64el (0.20.2-2) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:ppc64el (2.63.3-3) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.9ubuntu1) ... Setting up libbrotli1:ppc64el (1.0.7-6) ... Setting up libicu65:ppc64el (65.1-1ubuntu1) ... Setting up libnghttp2-14:ppc64el (1.40.0-1) ... Setting up libmagic1:ppc64el (1:5.38-4) ... Setting up libdeflate0 (1.5-3) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libldap-common (2.4.49+dfsg-1ubuntu1) ... Setting up libkrb5support0:ppc64el (1.17-6ubuntu4) ... Setting up libsasl2-modules-db:ppc64el (2.1.27+dfsg-2) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build1) ... Setting up libsigsegv2:ppc64el (2.12-2) ... Setting up libssl-dev:ppc64el (1.1.1d-2ubuntu3) ... Setting up autopoint (0.19.8.1-10) ... Setting up libk5crypto3:ppc64el (1.17-6ubuntu4) ... Setting up libsasl2-2:ppc64el (2.1.27+dfsg-2) ... Setting up libroken18-heimdal:ppc64el (7.7.0+dfsg-1) ... Setting up liblzma-dev:ppc64el (5.2.4-1) ... Setting up zlib1g-dev:ppc64el (1:1.2.11.dfsg-1ubuntu3) ... Setting up libuchardet0:ppc64el (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:ppc64el (1.17-6ubuntu4) ... Setting up libbsd0:ppc64el (0.10.0-1) ... Setting up libdeflate-dev:ppc64el (1.5-3) ... Setting up libelf1:ppc64el (0.176-1.1build1) ... Setting up libxml2:ppc64el (2.9.4+dfsg1-8ubuntu4) ... Setting up libheimbase1-heimdal:ppc64el (7.7.0+dfsg-1) ... Setting up libbz2-dev:ppc64el (1.0.8-2) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libtool (2.4.6-12) ... Setting up libasn1-8-heimdal:ppc64el (7.7.0+dfsg-1) ... Setting up m4 (1.4.18-4) ... Setting up libhcrypto4-heimdal:ppc64el (7.7.0+dfsg-1) ... Setting up libwind0-heimdal:ppc64el (7.7.0+dfsg-1) ... 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 libgssapi-krb5-2:ppc64el (1.17-6ubuntu4) ... Setting up libcroco3:ppc64el (0.6.13-1) ... Setting up libssh-4:ppc64el (0.9.3-2ubuntu1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10) ... Setting up libhx509-5-heimdal:ppc64el (7.7.0+dfsg-1) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libkrb5-26-heimdal:ppc64el (7.7.0+dfsg-1) ... Setting up po-debconf (1.0.21) ... Setting up libheimntlm0-heimdal:ppc64el (7.7.0+dfsg-1) ... Setting up libgssapi3-heimdal:ppc64el (7.7.0+dfsg-1) ... Setting up libldap-2.4-2:ppc64el (2.4.49+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:ppc64el (7.66.0-1ubuntu1) ... Setting up libcurl4-gnutls-dev:ppc64el (7.66.0-1ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.9ubuntu1) ... Setting up dh-exec (0.23.2) ... Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-173-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.34-1ubuntu1 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-28ubuntu1 gcc-9_9.2.1-28ubuntu1 libc6-dev_2.30-0ubuntu3 libstdc++-9-dev_9.2.1-28ubuntu1 libstdc++6_10-20200211-1ubuntu1 linux-libc-dev_5.4.0-14.17 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.9 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11ubuntu2 base-passwd_3.5.47 bash_5.0-5ubuntu1 binutils_2.34-1ubuntu1 binutils-common_2.34-1ubuntu1 binutils-powerpc64le-linux-gnu_2.34-1ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu6 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-28ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-exec_0.23.2 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7ubuntu2 dpkg-dev_1.19.7ubuntu2 dwz_0.13-5 e2fsprogs_1.45.3-4ubuntu3 fakeroot_1.24-1 fdisk_2.34-0.1ubuntu6 file_1:5.38-4 findutils_4.6.0+git+20190209-2ubuntu1 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-28ubuntu1 gcc_4:9.2.1-3.1ubuntu1 gcc-10-base_10-20200211-1ubuntu1 gcc-9_9.2.1-28ubuntu1 gcc-9-base_9.2.1-28ubuntu1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpg_2.2.17-3ubuntu1 gpg-agent_2.2.17-3ubuntu1 gpgconf_2.2.17-3ubuntu1 gpgv_2.2.17-3ubuntu1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-0ubuntu4 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5ubuntu1 libapparmor1_2.13.3-7ubuntu1 libapt-pkg5.90_1.9.9 libarchive-zip-perl_1.67-1 libargon2-1_0~20171227-0.2 libasan5_9.2.1-28ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-1 libassuan0_2.5.3-7ubuntu2 libatomic1_10-20200211-1ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu5 libaudit1_1:2.8.5-2ubuntu5 libbinutils_2.34-1ubuntu1 libblkid1_2.34-0.1ubuntu6 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libbz2-dev_1.0.8-2 libc-bin_2.30-0ubuntu3 libc-dev-bin_2.30-0ubuntu3 libc6_2.30-0ubuntu3 libc6-dev_2.30-0ubuntu3 libcap-ng0_0.7.9-2.1build1 libcap2_1:2.31-1 libcc1-0_10-20200211-1ubuntu1 libcom-err2_1.45.3-4ubuntu3 libcroco3_0.6.13-1 libcryptsetup12_2:2.2.2-3ubuntu1 libctf-nobfd0_2.34-1ubuntu1 libctf0_2.34-1ubuntu1 libcurl3-gnutls_7.66.0-1ubuntu1 libcurl4-gnutls-dev_7.66.0-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdebconfclient0_0.251ubuntu1 libdebhelper-perl_12.9ubuntu1 libdeflate-dev_1.5-3 libdeflate0_1.5-3 libdevmapper1.02.1_2:1.02.155-2ubuntu8 libdpkg-perl_1.19.7ubuntu2 libelf1_0.176-1.1build1 libext2fs2_1.45.3-4ubuntu3 libfakeroot_1.24-1 libfdisk1_2.34-0.1ubuntu6 libffi6_3.2.1-9 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libgcc-9-dev_9.2.1-28ubuntu1 libgcc-s1_10-20200211-1ubuntu1 libgcc1_1:10-20200211-1ubuntu1 libgcrypt20_1.8.5-3ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.63.3-3 libgmp10_2:6.2.0+dfsg-3 libgnutls30_3.6.11.1-2ubuntu2 libgomp1_10-20200211-1ubuntu1 libgpg-error0_1.36-7ubuntu1 libgssapi-krb5-2_1.17-6ubuntu4 libgssapi3-heimdal_7.7.0+dfsg-1 libhcrypto4-heimdal_7.7.0+dfsg-1 libheimbase1-heimdal_7.7.0+dfsg-1 libheimntlm0-heimdal_7.7.0+dfsg-1 libhogweed4_3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libhx509-5-heimdal_7.7.0+dfsg-1 libicu65_65.1-1ubuntu1 libidn2-0_2.2.0-2 libip4tc2_1.8.3-2ubuntu5 libisl21_0.21-2 libisl22_0.22-2 libitm1_10-20200211-1ubuntu1 libjson-c4_0.13.1+dfsg-6 libk5crypto3_1.17-6ubuntu4 libkeyutils1_1.6-6ubuntu1 libkmod2_26+20191223-1ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-1 libkrb5-3_1.17-6ubuntu4 libkrb5support0_1.17-6ubuntu4 libldap-2.4-2_2.4.49+dfsg-1ubuntu1 libldap-common_2.4.49+dfsg-1ubuntu1 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_10-20200211-1ubuntu1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1ubuntu6 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1ubuntu1 libncursesw6_6.1+20191019-1ubuntu1 libnettle6_3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnpth0_1.6-1 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.28_5.28.1-6build1 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libprocps7_2:3.3.15-2ubuntu3 libpsl5_0.20.2-2 libquadmath0_10-20200211-1ubuntu1 libreadline8_8.0-3 libroken18-heimdal_7.7.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2ubuntu2 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu6 libsqlite3-0_3.31.1-1ubuntu1 libss2_1.45.3-4ubuntu3 libssh-4_0.9.3-2ubuntu1 libssl-dev_1.1.1d-2ubuntu3 libssl1.1_1.1.1d-2ubuntu3 libstdc++-9-dev_9.2.1-28ubuntu1 libstdc++6_10-20200211-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_244.2-1ubuntu1 libtasn1-6_4.15.0-2 libtinfo6_6.1+20191019-1ubuntu1 libtool_2.4.6-12 libtsan0_10-20200211-1ubuntu1 libubsan1_10-20200211-1ubuntu1 libuchardet0_0.0.6-3 libudev1_244.2-1ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu6 libwind0-heimdal_7.7.0+dfsg-1 libxml2_2.9.4+dfsg1-8ubuntu4 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.0-14.17 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu1 logsave_1.45.3-4ubuntu3 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17ubuntu3 mount_2.34-0.1ubuntu6 ncurses-base_6.1+20191019-1ubuntu1 ncurses-bin_6.1+20191019-1ubuntu1 openssl_1.1.1d-2ubuntu3 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6build1 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 systemd_244.2-1ubuntu1 systemd-sysv_244.2-1ubuntu1 sysvinit-utils_2.96-2.1ubuntu1 tar_1.30+dfsg-6 tzdata_2019c-3 ubuntu-keyring_2020.02.11.1 util-linux_2.34-0.1ubuntu6 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 zlib1g-dev_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Feb 13 19:26:32 2020 UTC gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./htslib_1.10.2-2ubuntu2.dsc dpkg-source: info: extracting htslib in htslib-1.10.2 dpkg-source: info: unpacking htslib_1.10.2.orig.tar.bz2 dpkg-source: info: unpacking htslib_1.10.2-2ubuntu2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_git_version dpkg-source: info: applying define_PATH_MAX.patch dpkg-source: info: applying fPIC.patch dpkg-source: info: applying testShebang.patch dpkg-source: info: applying fix_float_precision dpkg-source: info: applying 1023.patch dpkg-source: info: applying debian-changes 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-18704120 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18704120 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18704120 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 1.10.2-2ubuntu2 dpkg-buildpackage: info: source distribution focal dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el dpkg-source: info: using options from htslib-1.10.2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j4 distclean make[2]: Entering directory '/<>' rm -f test/*.tmp test/*.tmp.* test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL* header-exports.txt shlib-exports-so.txt rm -f libhts.so libhts.so.* rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h rm -f hts-object-files rm -f libhts.a bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/sam test/test_bgzf test/test_kstring test/test_realn test/test-regidx test/test_str2int test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7 rm -f config.cache config.h config.log config.mk config.status rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk rm -rf autom4te.cache make[2]: Leaving directory '/<>' rm -rf test_backup/ make[1]: Leaving directory '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/libhts3.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files rm -fr -- debian/libhts3/ debian/tmp/ debian/libhts-dev/ debian/htslib-test/ debian/tabix/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a 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 --enable-gcs --enable-s3 ./configure --build=powerpc64le-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/powerpc64le-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3 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 pkg-config... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the compiler accepts -fvisibility=hidden... yes checking 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... yes checking for libdeflate_deflate_compress in -ldeflate... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking make[1]: Leaving directory '/<>' rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_build-arch 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)" \ PACKAGE_VERSION="1.10.2-2ubuntu2" \ libdir=/usr/lib/powerpc64le-linux-gnu make -j4 "CFLAGS=-g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto" PACKAGE_VERSION=1.10.2-2ubuntu2 libdir=/usr/lib/powerpc64le-linux-gnu make[2]: Entering directory '/<>' gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION_TEXT "1.10.2-2ubuntu2"' > version.h gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_libcurl.o hfile_libcurl.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_gcs.o hfile_gcs.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_s3.o hfile_s3.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile_s3_write.o hfile_s3_write.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o knetfile.pico knetfile.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_net.pico hfile_net.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kstring.o test/test_kstring.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_str2int.o test/test_str2int.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_index.o test/test_index.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -flto -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c gcc -shared -Wl,-soname,libhts.so.3 -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 header.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/string_alloc.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico hfile_s3_write.pico -ldeflate -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 -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_str2int test/test_str2int.o ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o ranlib libhts.a gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o bgzip bgzip.o libhts.a -ldeflate -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 -ldeflate -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 -ldeflate -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 -ldeflate -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 -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/pileup test/pileup.o libhts.a -ldeflate -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 -ldeflate -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 -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -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 -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread ln -sf libhts.so libhts.so.3 gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -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 -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test_index test/test_index.o libhts.a -ldeflate -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 -ldeflate -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 -ldeflate -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 -ldeflate -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 -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -Wl,-flto -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-arch make[1]: Entering directory '/<>' dh_auto_test || \ if find . -name "FAIL*" > /dev/null ; then \ for file in $(find . -name "FAIL*"); do echo ${file}; cat ${file}; done && false ; \ fi make -j4 test VERBOSE=1 make[2]: Entering directory '/<>' echo '#define HTS_VERSION_TEXT "1.10.2"' > version.h gcc -Wall -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o ranlib libhts.a gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/sam test/sam.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread test/hts_endian test/test_kstring test/test_str2int test/fieldarith test/fieldarith.sam test/hfile test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" Expected error: [E::hts_parse_region] Unexpected string "x" after region Expected error: [E::hts_parse_region] Unexpected string "y" after region Expected error: [E::hts_parse_region] Unexpected string "chr3" after region cd test/tabix && ./test-tabix.sh tabix.tst Testing tabix... PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 Expected passes: 13 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/mpileup && ./test-pileup.sh mpileup.tst Testing (m)pileup... PASS : $pileup mp_D.sam PASS : $pileup -m mp_D.sam PASS : $pileup mp_DI.sam PASS : $pileup -m mp_DI.sam PASS : $pileup mp_I.sam PASS : $pileup -m mp_I.sam PASS : $pileup mp_P.sam PASS : $pileup -m mp_P.sam PASS : $pileup mp_ID.sam PASS : $pileup -m mp_ID.sam PASS : $pileup mp_N.sam PASS : $pileup -m mp_N.sam PASS : $pileup mp_N2.sam PASS : $pileup -m mp_N2.sam PASS : $pileup c1#pad1.sam PASS : $pileup -m c1#pad1.sam PASS : $pileup c1#pad2.sam PASS : $pileup -m c1#pad2.sam PASS : $pileup c1#pad3.sam PASS : $pileup -m c1#pad3.sam PASS : $pileup -m small.bam Expected passes: 21 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx.fa test/fastqs.fq test/test-regidx cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} bgzip round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok test_index: /<>/test/test_view -l 0 -b -m 14 -x /tmp/sKG_wKRc5Q/index.bam.csi /<>/test/index.sam > /tmp/sKG_wKRc5Q/index.bam .. ok test_index: /<>/test/test_index -c /tmp/sKG_wKRc5Q/index.bam .. ok test_index: /<>/test/test_view -l 0 -b -m 0 -x /tmp/sKG_wKRc5Q/index.bam.bai /<>/test/index.sam > /tmp/sKG_wKRc5Q/index.bam .. ok test_index: /<>/test/test_index -b /tmp/sKG_wKRc5Q/index.bam .. ok test_index: /<>/test/test_view -l 0 -z -m 14 -x /tmp/sKG_wKRc5Q/index.sam.gz.csi /<>/test/index.sam > /tmp/sKG_wKRc5Q/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/sKG_wKRc5Q/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 0 -x /tmp/sKG_wKRc5Q/index.sam.gz.bai /<>/test/index.sam > /tmp/sKG_wKRc5Q/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/sKG_wKRc5Q/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -C -x /tmp/sKG_wKRc5Q/index.cram.crai /<>/test/index.sam > /tmp/sKG_wKRc5Q/index.cram .. ok test_index: /<>/test/test_index /tmp/sKG_wKRc5Q/index.cram .. ok test_index: /<>/test/test_view -l 0 -b -m 14 -x /tmp/sKG_wKRc5Q/index.bcf.csi /<>/test/index.vcf > /tmp/sKG_wKRc5Q/index.bcf .. ok test_index: /<>/test/test_index -c /tmp/sKG_wKRc5Q/index.bcf .. ok test_index: /<>/test/test_view -l 0 -z -m 14 -x /tmp/sKG_wKRc5Q/index.vcf.gz.csi /<>/test/index.vcf > /tmp/sKG_wKRc5Q/index.vcf.gz .. ok test_index: /<>/test/test_index -c /tmp/sKG_wKRc5Q/index.vcf.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 0 -x /tmp/sKG_wKRc5Q/index.vcf.gz.tbi /<>/test/index.vcf > /tmp/sKG_wKRc5Q/index.vcf.gz .. ok test_index: /<>/test/test_index -t /tmp/sKG_wKRc5Q/index.vcf.gz .. ok test_index: /<>/tabix /tmp/sKG_wKRc5Q/index.vcf.gz##idx##/tmp/sKG_wKRc5Q/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /<>/test/test_view -@4 -l 0 -b -m 14 -x /tmp/sKG_wKRc5Q/index.bam.csi /<>/test/index.sam > /tmp/sKG_wKRc5Q/index.bam .. ok test_index: /<>/test/test_index -c /tmp/sKG_wKRc5Q/index.bam .. ok test_index: /<>/test/test_view -@4 -l 0 -b -m 0 -x /tmp/sKG_wKRc5Q/index.bam.bai /<>/test/index.sam > /tmp/sKG_wKRc5Q/index.bam .. ok test_index: /<>/test/test_index -b /tmp/sKG_wKRc5Q/index.bam .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/sKG_wKRc5Q/index.sam.gz.csi /<>/test/index.sam > /tmp/sKG_wKRc5Q/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/sKG_wKRc5Q/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/sKG_wKRc5Q/index.sam.gz.bai /<>/test/index.sam > /tmp/sKG_wKRc5Q/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/sKG_wKRc5Q/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -C -x /tmp/sKG_wKRc5Q/index.cram.crai /<>/test/index.sam > /tmp/sKG_wKRc5Q/index.cram .. ok test_index: /<>/test/test_index /tmp/sKG_wKRc5Q/index.cram .. ok test_index: /<>/test/test_view -@4 -l 0 -b -m 14 -x /tmp/sKG_wKRc5Q/index.bcf.csi /<>/test/index.vcf > /tmp/sKG_wKRc5Q/index.bcf .. ok test_index: /<>/test/test_index -c /tmp/sKG_wKRc5Q/index.bcf .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/sKG_wKRc5Q/index.vcf.gz.csi /<>/test/index.vcf > /tmp/sKG_wKRc5Q/index.vcf.gz .. ok test_index: /<>/test/test_index -c /tmp/sKG_wKRc5Q/index.vcf.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/sKG_wKRc5Q/index.vcf.gz.tbi /<>/test/index.vcf > /tmp/sKG_wKRc5Q/index.vcf.gz .. ok test_index: /<>/test/test_index -t /tmp/sKG_wKRc5Q/index.vcf.gz .. ok test_index: /<>/tabix /tmp/sKG_wKRc5Q/index.vcf.gz##idx##/tmp/sKG_wKRc5Q/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_view testing multi-ref CRAM modes: ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing multi-ref CRAM modes: ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -t auxf.fa -S -l0 -C -o VERSION=3.0 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram ./test_view -t auxf.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram ./test_view auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram ./test_view c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram ./test_view c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram ./test_view c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram ./test_view c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram ./test_view c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram ./test_view c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -S -l0 -C -o VERSION=3.0 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram ./test_view -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram ./test_view c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -t c2.fa -S -l0 -C -o VERSION=3.0 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram ./test_view -t c2.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram ./test_view c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram ./test_view ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam ./test_view ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam ./test_view ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.cram > ce#1000.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram ./test_view ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram ./test_view ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram ./test_view ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram ./test_view ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram ./test_view ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram ./test_view ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram ./test_view ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram ./test_view ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram ./test_view ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram ./test_view ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram ./test_view -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram ./test_view ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=2.1 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam ./test_view md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -t md.fa -S -l0 -C -o VERSION=3.0 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam ./test_view md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -t md.fa -C -o VERSION=2.1 md#1.tmp.cram > md#1.tmp.cram.cram ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.cram.cram > md#1.tmp.cram ./test_view -t md.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram ./test_view md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram ./test_view xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram ./test_view xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram ./test_view xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -S -b xx#MD.sam > xx#MD.tmp.bam ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam ./test_view xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD.sam > xx#MD.tmp.cram ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam ./test_view xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#MD.tmp.cram > xx#MD.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram.cram > xx#MD.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram ./test_view xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -S -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam ./test_view xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam ./test_view xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram ./test_view xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram ./test_view xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram ./test_view xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram ./test_view xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram ./test_view xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram ./test_view xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram ./test_view xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram ./test_view xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -S -l0 -C -o VERSION=3.0 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram ./test_view -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram ./test_view xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ .. ok test_view testing region queries: ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out .. ok test_view testing BAM files with absent @SQ lines: ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /<>/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -@4 -S -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view -@4 auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -S -l0 -C -o VERSION=3.0 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam ./test_view -@4 auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 auxf#values.tmp.cram.cram > auxf#values.tmp.cram ./test_view -@4 auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -@4 -S -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view -@4 c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam ./test_view -@4 c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram ./test_view -@4 c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view -@4 c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam ./test_view -@4 c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#clip.tmp.cram.cram > c1#clip.tmp.cram ./test_view -@4 c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view -@4 c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam ./test_view -@4 c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram ./test_view -@4 c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view -@4 c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam ./test_view -@4 c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram ./test_view -@4 c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view -@4 c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam ./test_view -@4 c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram ./test_view -@4 c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view -@4 c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam ./test_view -@4 c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram ./test_view -@4 c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -@4 -S -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view -@4 c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l0 -C -o VERSION=3.0 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam ./test_view -@4 c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram ./test_view -@4 -t c1.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram ./test_view -@4 c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view -@4 c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c2.fa -S -l0 -C -o VERSION=3.0 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam ./test_view -@4 c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram ./test_view -@4 -t c2.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 c2#pad.tmp.cram.cram > c2#pad.tmp.cram ./test_view -@4 c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view -@4 ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam ./test_view -@4 ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1.tmp.cram.cram > ce#1.tmp.cram ./test_view -@4 ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam ./test_view -@4 ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 -b -D ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam ./test_view -@4 ce#1000.tmp.bam.cram.bam > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#1000.tmp.cram > ce#1000.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.cram.cram > ce#1000.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.cram.cram > ce#1000.tmp.cram ./test_view -@4 ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view -@4 ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam ./test_view -@4 ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#2.tmp.cram.cram > ce#2.tmp.cram ./test_view -@4 ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view -@4 ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam ./test_view -@4 ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.cram.cram > ce#5.tmp.cram ./test_view -@4 ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -@4 -S -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view -@4 ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam ./test_view -@4 ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.cram.cram > ce#5b.tmp.cram ./test_view -@4 ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -@4 -S -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view -@4 ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam ./test_view -@4 ce#large_seq.tmp.bam.cram.bam > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram ./test_view -@4 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -@4 -S -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view -@4 ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam ./test_view -@4 ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#supp.tmp.cram.cram > ce#supp.tmp.cram ./test_view -@4 ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -@4 -S -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view -@4 ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam ./test_view -@4 ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram ./test_view -@4 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view -@4 ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam ./test_view -@4 ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram ./test_view -@4 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view -@4 ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam ./test_view -@4 ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram ./test_view -@4 ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view -@4 ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam ./test_view -@4 ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram ./test_view -@4 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view -@4 ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam ./test_view -@4 ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram ./test_view -@4 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=2.1 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam ./test_view -@4 md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t md.fa -S -l0 -C -o VERSION=3.0 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 -b -D md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam ./test_view -@4 md#1.tmp.bam.cram.bam > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t md.fa -C -o VERSION=2.1 md#1.tmp.cram > md#1.tmp.cram.cram ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.cram.cram > md#1.tmp.cram ./test_view -@4 -t md.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 md#1.tmp.cram.cram > md#1.tmp.cram ./test_view -@4 md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view -@4 xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam ./test_view -@4 xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.cram.cram > xx#blank.tmp.cram ./test_view -@4 xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -@4 -S -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view -@4 xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam ./test_view -@4 xx#large_aux.tmp.bam.cram.bam > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram ./test_view -@4 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -@4 -S -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view -@4 xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam ./test_view -@4 xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram ./test_view -@4 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -@4 -S -b xx#MD.sam > xx#MD.tmp.bam ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam ./test_view -@4 xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 -b -D xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam ./test_view -@4 xx#MD.tmp.bam.cram.bam > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD.tmp.cram > xx#MD.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.cram.cram > xx#MD.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD.tmp.cram.cram > xx#MD.tmp.cram ./test_view -@4 xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -@4 -S -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam ./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 -b -D xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam ./test_view -@4 xx#MD2.tmp.bam.cram.bam > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#MD2.tmp.cram > xx#MD2.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#MD2.tmp.cram.cram > xx#MD2.tmp.cram ./test_view -@4 xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view -@4 xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam ./test_view -@4 xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram ./test_view -@4 xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view -@4 xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam ./test_view -@4 xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#pair.tmp.cram.cram > xx#pair.tmp.cram ./test_view -@4 xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -@4 -S -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view -@4 xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam ./test_view -@4 xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram ./test_view -@4 xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view -@4 xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam ./test_view -@4 xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#rg.tmp.cram.cram > xx#rg.tmp.cram ./test_view -@4 xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view -@4 xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam ./test_view -@4 xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram ./test_view -@4 xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -@4 -S -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view -@4 xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam ./test_view -@4 xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram ./test_view -@4 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view -@4 xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam ./test_view -@4 xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram ./test_view -@4 xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view -@4 xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l0 -C -o VERSION=3.0 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam ./test_view -@4 xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram ./test_view -@4 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ .. ok test_view testing region queries: ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out .. ok test_view testing BAM files with absent @SQ lines: ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /<>/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_MD testing xx#MD.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ Checking for MD/NM in xx#MD.sam ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_MD testing xx#MD2.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_vcf_api: /<>/test/test-vcf-api /tmp/sKG_wKRc5Q/test-vcf-api.bcf [E::bcf_index_build3] TBI indices for BCF files are not supported [E::idx_find_and_load] Could not retrieve index file for '/tmp/sKG_wKRc5Q/test-vcf-api.bcf' .. ok test_vcf_sweep: /<>/test/test-vcf-sweep /tmp/sKG_wKRc5Q/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/sKG_wKRc5Q -s 1554074593 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/sKG_wKRc5Q -s 463344015 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/sKG_wKRc5Q -s 1358276230 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/sKG_wKRc5Q -s 1256176785 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/sKG_wKRc5Q -s 574216643 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/sKG_wKRc5Q -s 637285547 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/sKG_wKRc5Q -s 333482429 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/sKG_wKRc5Q -s 1438958866 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/sKG_wKRc5Q -s 1280578718 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/sKG_wKRc5Q -s 1195570064 .. ok test_command: /<>/test/test-bcf-translate - .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/sKG_wKRc5Q/headernul0.bam .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/sKG_wKRc5Q/headernul1.bam .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/sKG_wKRc5Q/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /<>/bgzip -I /<>/test/bgziptest.txt.tmp.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 .. 153 passed .. 153 failed .. 0 make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a rm -f -- debian/libhts3.substvars debian/libhts-dev.substvars debian/tabix.substvars rm -fr -- debian/.debhelper/generated/libhts3/ debian/libhts3/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/tabix/ debian/tabix/ rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_install-arch 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 install -d /<>/debian/tmp make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/<>' mkdir -p -m 755 /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/include /<>/debian/tmp/usr/include/htslib /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu /<>/debian/tmp/usr/share/man/man1 /<>/debian/tmp/usr/share/man/man5 /<>/debian/tmp/usr/share/man/man7 /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/pkgconfig gcc -Wall -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -fvisibility=hidden -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 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/powerpc64le-linux-gnu#g;s#@-PACKAGE_VERSION@#1.10.2#g' htslib.pc.tmp > /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/pkgconfig/htslib.pc chmod 644 /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/pkgconfig/htslib.pc gcc -shared -Wl,-soname,libhts.so.3 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/string_alloc.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico hfile_s3_write.pico -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread ln -sf libhts.so libhts.so.3 install -p -m 644 libhts.so /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.so.1.10.2 ln -sf libhts.so.1.10.2 /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.so ln -sf libhts.so.1.10.2 /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.so.3 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/powerpc64le-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 install -p -m 644 htslib-s3-plugin.7 /<>/debian/tmp/usr/share/man/man7 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 -a install -d debian/libhts3/usr/lib/powerpc64le-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.so.1.10.2 debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.so.3 debian/libhts3/usr/lib/powerpc64le-linux-gnu/ install -d debian/.debhelper/generated/libhts3 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/powerpc64le-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.a debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.so debian/libhts-dev/usr/lib/powerpc64le-linux-gnu/ install -d debian/libhts-dev/usr/lib/powerpc64le-linux-gnu/pkgconfig cp --reflink=auto -a debian/tmp/usr/lib/powerpc64le-linux-gnu/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/powerpc64le-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/.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 rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_installdocs make[1]: Entering directory '/<>' dh_installdocs install -d debian/libhts3/usr/share/doc/libhts3 install -p -m0644 debian/copyright debian/libhts3/usr/share/doc/libhts3/copyright install -d debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/README.test debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README.large_positions.md debian/libhts-dev/usr/share/doc/libhts-dev 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/tabix/usr/share/doc/tabix install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright # Fix Perl interpreter path for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/libhts-dev/usr/lib/powerpc64le-linux-gnu/libhts.so: No such file or directory make[1]: Leaving directory '/<>' rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs NEWS install -p -m0644 debian/changelog debian/libhts3/usr/share/doc/libhts3/changelog.Debian install -p -m0644 NEWS debian/libhts3/usr/share/doc/libhts3/changelog install -p -m0644 debian/changelog debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog install -p -m0644 debian/changelog debian/tabix/usr/share/doc/tabix/changelog.Debian install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog make[1]: Leaving directory '/<>' dh_installman -a 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-recode --to-code UTF-8 --suffix .dh-new debian/libhts-dev/usr/share/man/man5/vcf.5 debian/tabix/usr/share/man/man1/htsfile.1 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts-dev/usr/share/man/man5/faidx.5 debian/libhts-dev/usr/share/man/man5/sam.5 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/tabix.1 mv debian/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1 chmod 0644 -- debian/tabix/usr/share/man/man1/tabix.1 mv debian/libhts-dev/usr/share/man/man5/faidx.5.dh-new debian/libhts-dev/usr/share/man/man5/faidx.5 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/faidx.5 debian/libhts-dev/usr/share/man/man5/sam.5 mv debian/libhts-dev/usr/share/man/man5/vcf.5.dh-new debian/libhts-dev/usr/share/man/man5/vcf.5 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/vcf.5 debian/tabix/usr/share/man/man1/htsfile.1 dh_perl -a dh_link -a rm -f debian/libhts3/usr/lib/powerpc64le-linux-gnu/libhts.so.3 ln -s libhts.so.1.10.2 debian/libhts3/usr/lib/powerpc64le-linux-gnu/libhts.so.3 rm -f debian/libhts-dev/usr/lib/powerpc64le-linux-gnu/libhts.so ln -s libhts.so.1.10.2 debian/libhts-dev/usr/lib/powerpc64le-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 -a dh_compress -a cd debian/libhts3 cd debian/tabix cd debian/libhts-dev 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 cd '/<>' chmod a-x usr/share/doc/libhts3/changelog usr/share/doc/libhts3/changelog.Debian chmod a-x usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 gzip -9nf usr/share/doc/libhts3/changelog usr/share/doc/libhts3/changelog.Debian gzip -9nf usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 cd '/<>' cd '/<>' rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian/libhts3 -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/libhts-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/libhts3 ! -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-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts3/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts3/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts3 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libhts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x 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/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian -name simple_test_driver.sh -exec chmod +x \{\} \; make[1]: Leaving directory '/<>' dh_missing -a dh_missing: warning: usr/bin/tabix exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/bin/htsfile exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/bin/bgzip exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/man/man1/htsfile.1 exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/man/man1/bgzip.1 exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/man/man1/tabix.1 exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/man/man7/htslib-s3-plugin.7 exists in debian/tmp but is not installed to anywhere The following debhelper tools have reported what they installed (with files per package) * dh_install: htslib-test (219), libhts-dev (7), libhts3 (2), tabix (3) * dh_installdocs: htslib-test (0), libhts-dev (3), libhts3 (0), tabix (0) * dh_installman: htslib-test (0), libhts-dev (0), libhts3 (0), tabix (2) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built For a short-term work-around: Add the files to debian/not-installed dh_dwz -a dwz -- debian/libhts3/usr/lib/powerpc64le-linux-gnu/libhts.so.1.10.2 install -d debian/tabix/usr/lib/debug/.dwz/powerpc64le-linux-gnu dwz -mdebian/tabix/usr/lib/debug/.dwz/powerpc64le-linux-gnu/tabix.debug -M/usr/lib/debug/.dwz/powerpc64le-linux-gnu/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/powerpc64le-linux-gnu/tabix.debug dh_strip -a install -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/b2 objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/powerpc64le-linux-gnu/libhts.so.1.10.2 debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/b2/6d275b0d9a7913fb60fc8931c33adbe79cdf64.debug strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/libhts-dev/usr/lib/powerpc64le-linux-gnu/libhts.a install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/25 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/25/5a575d342eb95f217e1d374f32a44bbe540104.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/25/5a575d342eb95f217e1d374f32a44bbe540104.debug chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/25/5a575d342eb95f217e1d374f32a44bbe540104.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/25/5a575d342eb95f217e1d374f32a44bbe540104.debug debian/tabix/usr/bin/tabix install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/65 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/65/bdeaf81846216418d2b0732ebd33417ca74a2a.debug chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/b2/6d275b0d9a7913fb60fc8931c33adbe79cdf64.debug chown 0:0 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/b2/6d275b0d9a7913fb60fc8931c33adbe79cdf64.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/powerpc64le-linux-gnu/libhts.so.1.10.2 objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/b2/6d275b0d9a7913fb60fc8931c33adbe79cdf64.debug debian/libhts3/usr/lib/powerpc64le-linux-gnu/libhts.so.1.10.2 install -d debian/.debhelper/libhts3/dbgsym-root/usr/share/doc ln -s libhts3 debian/.debhelper/libhts3/dbgsym-root/usr/share/doc/libhts3-dbgsym chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/65/bdeaf81846216418d2b0732ebd33417ca74a2a.debug chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/65/bdeaf81846216418d2b0732ebd33417ca74a2a.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/65/bdeaf81846216418d2b0732ebd33417ca74a2a.debug debian/tabix/usr/bin/htsfile install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/31 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/31/881668020fb7a582e5fa4fdc174a272ed991a4.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/31/881668020fb7a582e5fa4fdc174a272ed991a4.debug chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/31/881668020fb7a582e5fa4fdc174a272ed991a4.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/31/881668020fb7a582e5fa4fdc174a272ed991a4.debug debian/tabix/usr/bin/bgzip install -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/powerpc64le-linux-gnu debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/tabix/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/tabix/usr/lib/debug install -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym dh_makeshlibs -a rm -f debian/libhts3/DEBIAN/shlibs install -d debian/libhts3/DEBIAN echo "libhts 3 libhts3 (>= 1.10.2)" >> debian/libhts3/DEBIAN/shlibs chmod 0644 -- debian/libhts3/DEBIAN/shlibs chown 0:0 -- debian/libhts3/DEBIAN/shlibs dpkg-gensymbols -plibhts3 -Idebian/libhts3.symbols -Pdebian/libhts3 -edebian/libhts3/usr/lib/powerpc64le-linux-gnu/libhts.so.1.10.2 mv debian/.debhelper/generated/libhts3/triggers.new debian/.debhelper/generated/libhts3/triggers rm -f debian/libhts-dev/DEBIAN/shlibs rm -f debian/tabix/DEBIAN/shlibs dh_shlibdeps -a dpkg-shlibdeps -Tdebian/libhts3.substvars debian/libhts3/usr/lib/powerpc64le-linux-gnu/libhts.so.1.10.2 install -d debian/tabix/DEBIAN dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/tabix debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/bgzip dh_installdeb -a install -p -m0644 debian/.debhelper/generated/libhts3/triggers debian/libhts3/DEBIAN/triggers install -d debian/libhts-dev/DEBIAN dh_gencontrol -a 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 echo misc:Depends= >> debian/libhts3.substvars echo misc:Pre-Depends= >> debian/libhts3.substvars install -d debian/.debhelper/libhts3/dbgsym-root/DEBIAN dpkg-gencontrol -plibhts3 -ldebian/changelog -Tdebian/libhts3.substvars -Pdebian/.debhelper/libhts3/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -DPackage=libhts3-dbgsym "-DDepends=libhts3 (= \${binary:Version})" "-DDescription=debug symbols for libhts3" -DBuild-Ids=b26d275b0d9a7913fb60fc8931c33adbe79cdf64 -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 -UBuilt-Using -DAuto-Built-Package=debug-symbols -DPackage=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=255a575d342eb95f217e1d374f32a44bbe540104 31881668020fb7a582e5fa4fdc174a272ed991a4 65bdeaf81846216418d2b0732ebd33417ca74a2a" -DSection=debug -DPackage-Type=ddeb -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibhts3 -ldebian/changelog -Tdebian/libhts3.substvars -Pdebian/libhts3 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/libhts-dev/DEBIAN/control chown 0:0 -- debian/libhts-dev/DEBIAN/control chmod 0644 -- debian/tabix/DEBIAN/control chown 0:0 -- debian/tabix/DEBIAN/control chmod 0644 -- debian/libhts3/DEBIAN/control chown 0:0 -- debian/libhts3/DEBIAN/control dh_md5sums -a cd debian/libhts3 >/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 cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts3/DEBIAN/md5sums chown 0:0 -- debian/libhts3/DEBIAN/md5sums cd debian/.debhelper/libhts3/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums chown 0:0 -- debian/libhts-dev/DEBIAN/md5sums chmod 0644 -- debian/tabix/DEBIAN/md5sums chown 0:0 -- debian/tabix/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/md5sums cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --build debian/libhts3 .. dpkg-deb --build debian/libhts-dev .. 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 144 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing libhts-dev (in debian/libhts-dev); do_strip: , oemstrip: pkgstriptranslations: processing libhts3 (in debian/libhts3); do_strip: , oemstrip: pkgstriptranslations: processing tabix-dbgsym (in debian/.debhelper/tabix/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/tabix/dbgsym-root/DEBIAN/control, package tabix-dbgsym, directory debian/.debhelper/tabix/dbgsym-root pkgstripfiles: processing control file: debian/libhts-dev/DEBIAN/control, package libhts-dev, directory debian/libhts-dev dpkg-deb: building package 'tabix-dbgsym' in 'debian/.debhelper/scratch-space/build-tabix/tabix-dbgsym_1.10.2-2ubuntu2_ppc64el.deb'. .. removing usr/share/doc/libhts-dev/changelog.gz INFO: pkgstripfiles: waiting for lock (libhts-dev) ... Renaming tabix-dbgsym_1.10.2-2ubuntu2_ppc64el.deb to tabix-dbgsym_1.10.2-2ubuntu2_ppc64el.ddeb mv debian/.debhelper/scratch-space/build-tabix/tabix-dbgsym_1.10.2-2ubuntu2_ppc64el.deb ../tabix-dbgsym_1.10.2-2ubuntu2_ppc64el.ddeb INFO: pkgstripfiles: waiting for lock (libhts-dev) ... INFO: pkgstripfiles: waiting for lock (libhts-dev) ... INFO: pkgstripfiles: waiting for lock (libhts-dev) ... INFO: pkgstripfiles: waiting for lock (libhts-dev) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libhts3/DEBIAN/control, package libhts3, directory debian/libhts3 .. removing usr/share/doc/libhts3/changelog.gz pkgstripfiles: Truncating usr/share/doc/libhts3/changelog.Debian.gz to topmost ten records INFO: pkgstripfiles: waiting for lock (libhts-dev) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package libhts3 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libhts3' in '../libhts3_1.10.2-2ubuntu2_ppc64el.deb'. install -d debian/.debhelper/scratch-space/build-libhts3 dpkg-deb --build debian/.debhelper/libhts3/dbgsym-root debian/.debhelper/scratch-space/build-libhts3 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing libhts3-dbgsym (in debian/.debhelper/libhts3/dbgsym-root); do_strip: , oemstrip: Searching for duplicated docs in dependency libhts3... symlinking changelog.Debian.gz in libhts-dev to file in libhts3 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libhts-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.10.2-2ubuntu2_ppc64el.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " dpkg-deb --build debian/tabix .. pkgstripfiles: processing control file: debian/.debhelper/libhts3/dbgsym-root/DEBIAN/control, package libhts3-dbgsym, directory debian/.debhelper/libhts3/dbgsym-root dpkg-deb: building package 'libhts3-dbgsym' in 'debian/.debhelper/scratch-space/build-libhts3/libhts3-dbgsym_1.10.2-2ubuntu2_ppc64el.deb'. INFO: pkgstriptranslations version 144 pkgstriptranslations: processing tabix (in debian/tabix); do_strip: , oemstrip: Renaming libhts3-dbgsym_1.10.2-2ubuntu2_ppc64el.deb to libhts3-dbgsym_1.10.2-2ubuntu2_ppc64el.ddeb mv debian/.debhelper/scratch-space/build-libhts3/libhts3-dbgsym_1.10.2-2ubuntu2_ppc64el.deb ../libhts3-dbgsym_1.10.2-2ubuntu2_ppc64el.ddeb 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_1.10.2-2ubuntu2_ppc64el.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../htslib_1.10.2-2ubuntu2_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-source: info: using options from htslib-1.10.2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20200213-1942 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ htslib_1.10.2-2ubuntu2_ppc64el.changes: --------------------------------------- Format: 1.8 Date: Thu, 13 Feb 2020 20:25:47 +0100 Source: htslib Binary: libhts-dev libhts3 tabix Architecture: ppc64el Version: 1.10.2-2ubuntu2 Distribution: focal-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Gianfranco Costamagna Description: libhts-dev - development files for the HTSlib libhts3 - C library for high-throughput sequencing data formats tabix - generic indexer for TAB-delimited genome position files Changes: htslib (1.10.2-2ubuntu2) focal; urgency=medium . * debian/patches/1023.patch: - cherry-pick upstream proposed patch for Big Endian fixes. Checksums-Sha1: 26203530d9b969108f186286350701f939538d22 7446 htslib_1.10.2-2ubuntu2_ppc64el.buildinfo 36c1d6d0757515418d60f88c4c933d5302bb13a8 92016 libhts-dev_1.10.2-2ubuntu2_ppc64el.deb bf408fda2cbab3f44844547d9f361f4e2f82fa79 1170820 libhts3-dbgsym_1.10.2-2ubuntu2_ppc64el.ddeb 94e49201fed6a998621aac30575cd7c1e1f66937 407196 libhts3_1.10.2-2ubuntu2_ppc64el.deb d258cf66ef7dc59889540447e471e612e047bf5d 1781884 tabix-dbgsym_1.10.2-2ubuntu2_ppc64el.ddeb c8b51220d281006e55f28ba5314362e9b0c1fc94 407704 tabix_1.10.2-2ubuntu2_ppc64el.deb Checksums-Sha256: a001f6a49dceafee8f9f33cc82abbe0f5e517c39dd4dfa37e9a7059aad3a630a 7446 htslib_1.10.2-2ubuntu2_ppc64el.buildinfo c2378d4e7c43f087962c1e6871f508b71ffa8107b8265ee137f38d7d1625fd36 92016 libhts-dev_1.10.2-2ubuntu2_ppc64el.deb fe9a6bb0cb86eb186901d5eebe3656e1401291fdb68bde7b90a9f87e35715274 1170820 libhts3-dbgsym_1.10.2-2ubuntu2_ppc64el.ddeb 5e22352bebba08b3fae0a727ddcf155d27ffcb0c112aa8a4730a47634a83b002 407196 libhts3_1.10.2-2ubuntu2_ppc64el.deb 24b98ec6cef4729fca9ccb56a19b40579db22b5c858cc21f95f43a3e3b0eeafb 1781884 tabix-dbgsym_1.10.2-2ubuntu2_ppc64el.ddeb 804d9725d4572cfe34719f40b84bb0144a05a6cde441d67f4cbd3bbe4b33fa3a 407704 tabix_1.10.2-2ubuntu2_ppc64el.deb Files: cdfa1ef37fecc3819a976526146a393a 7446 science optional htslib_1.10.2-2ubuntu2_ppc64el.buildinfo dccb2b36ad381bc6f275cd32a66af70d 92016 libdevel optional libhts-dev_1.10.2-2ubuntu2_ppc64el.deb 9ad437f19b3f5122ce8492131e8d293f 1170820 debug optional libhts3-dbgsym_1.10.2-2ubuntu2_ppc64el.ddeb c03020ec623b24d6d918265d055bc463 407196 libs optional libhts3_1.10.2-2ubuntu2_ppc64el.deb 26b4e7f980438c0300a9e1cb052a3f7c 1781884 debug optional tabix-dbgsym_1.10.2-2ubuntu2_ppc64el.ddeb ec58978a4a10c77274e2f6a2efcbe741 407704 science optional tabix_1.10.2-2ubuntu2_ppc64el.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libhts-dev_1.10.2-2ubuntu2_ppc64el.deb -------------------------------------- new debian package, version 2.0. size 92016 bytes: control archive=1920 bytes. 1144 bytes, 25 lines control 2266 bytes, 35 lines md5sums Package: libhts-dev Source: htslib Version: 1.10.2-2ubuntu2 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 457 Depends: libhts3 (= 1.10.2-2ubuntu2), 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 2020-02-13 19:25 ./ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/include/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/include/htslib/ -rw-r--r-- root/root 16101 2019-11-19 11:20 ./usr/include/htslib/bgzf.h -rw-r--r-- root/root 15928 2019-11-26 21:07 ./usr/include/htslib/cram.h -rw-r--r-- root/root 12245 2019-11-26 21:07 ./usr/include/htslib/faidx.h -rw-r--r-- root/root 10979 2019-11-19 11:20 ./usr/include/htslib/hfile.h -rw-r--r-- root/root 48171 2019-12-19 09:52 ./usr/include/htslib/hts.h -rw-r--r-- root/root 3889 2019-11-19 11:20 ./usr/include/htslib/hts_defs.h -rw-r--r-- root/root 11446 2017-09-27 15:40 ./usr/include/htslib/hts_endian.h -rw-r--r-- root/root 3944 2019-10-01 22:06 ./usr/include/htslib/hts_log.h -rw-r--r-- root/root 2124 2019-11-19 11:20 ./usr/include/htslib/hts_os.h -rw-r--r-- root/root 5603 2019-11-19 11:20 ./usr/include/htslib/kbitset.h -rw-r--r-- root/root 2828 2019-11-19 11:20 ./usr/include/htslib/kfunc.h -rw-r--r-- root/root 22882 2019-11-19 11:20 ./usr/include/htslib/khash.h -rw-r--r-- root/root 3995 2019-11-19 11:20 ./usr/include/htslib/khash_str2int.h -rw-r--r-- root/root 5135 2019-11-19 11:20 ./usr/include/htslib/klist.h -rw-r--r-- root/root 2972 2019-11-19 11:20 ./usr/include/htslib/knetfile.h -rw-r--r-- root/root 9186 2019-11-19 11:20 ./usr/include/htslib/kseq.h -rw-r--r-- root/root 11480 2019-11-19 11:20 ./usr/include/htslib/ksort.h -rw-r--r-- root/root 11416 2019-12-06 12:42 ./usr/include/htslib/kstring.h -rw-r--r-- root/root 8913 2019-11-26 21:07 ./usr/include/htslib/regidx.h -rw-r--r-- root/root 67260 2019-11-26 21:07 ./usr/include/htslib/sam.h -rw-r--r-- root/root 15605 2019-11-26 21:07 ./usr/include/htslib/synced_bcf_reader.h -rw-r--r-- root/root 4925 2019-11-26 21:07 ./usr/include/htslib/tbx.h -rw-r--r-- root/root 12492 2019-11-26 21:07 ./usr/include/htslib/thread_pool.h -rw-r--r-- root/root 59787 2020-02-13 19:25 ./usr/include/htslib/vcf.h -rw-r--r-- root/root 1681 2019-11-19 11:20 ./usr/include/htslib/vcf_sweep.h -rw-r--r-- root/root 4925 2019-10-01 22:06 ./usr/include/htslib/vcfutils.h drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/lib/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/lib/powerpc64le-linux-gnu/ -rw-r--r-- root/root 24250 2020-02-13 19:25 ./usr/lib/powerpc64le-linux-gnu/libhts.a lrwxrwxrwx root/root 0 2020-02-13 19:25 ./usr/lib/powerpc64le-linux-gnu/libhts.so -> libhts.so.1.10.2 drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/lib/powerpc64le-linux-gnu/pkgconfig/ -rw-r--r-- root/root 638 2020-02-13 19:25 ./usr/lib/powerpc64le-linux-gnu/pkgconfig/htslib.pc drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/share/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/share/doc/libhts-dev/ -rw-r--r-- root/root 273 2014-08-15 09:12 ./usr/share/doc/libhts-dev/README -rw-r--r-- root/root 2961 2019-12-10 17:59 ./usr/share/doc/libhts-dev/README.large_positions.md.gz -rw-r--r-- root/root 401 2019-09-04 08:27 ./usr/share/doc/libhts-dev/README.test lrwxrwxrwx root/root 0 2020-02-13 19:25 ./usr/share/doc/libhts-dev/changelog.Debian.gz -> ../libhts3/changelog.Debian.gz -rw-r--r-- root/root 5762 2019-09-04 08:27 ./usr/share/doc/libhts-dev/copyright drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/share/man/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/share/man/man5/ -rw-r--r-- root/root 2452 2020-02-13 19:25 ./usr/share/man/man5/faidx.5.gz -rw-r--r-- root/root 1539 2020-02-13 19:25 ./usr/share/man/man5/sam.5.gz -rw-r--r-- root/root 1857 2020-02-13 19:25 ./usr/share/man/man5/vcf.5.gz libhts3_1.10.2-2ubuntu2_ppc64el.deb ----------------------------------- new debian package, version 2.0. size 407196 bytes: control archive=4604 bytes. 1242 bytes, 23 lines control 223 bytes, 3 lines md5sums 29 bytes, 1 lines shlibs 21077 bytes, 758 lines symbols 72 bytes, 2 lines triggers Package: libhts3 Source: htslib Version: 1.10.2-2ubuntu2 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1214 Depends: libbz2-1.0, libc6 (>= 2.29), libcurl3-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), liblzma5 (>= 5.1.1alpha+20120614), libssl1.1 (>= 1.1.0), zlib1g (>= 1:1.2.0) Breaks: libtabixpp (<< 1.0.0-5~), 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 2020-02-13 19:25 ./ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/lib/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/lib/powerpc64le-linux-gnu/ -rw-r--r-- root/root 1181744 2020-02-13 19:25 ./usr/lib/powerpc64le-linux-gnu/libhts.so.1.10.2 lrwxrwxrwx root/root 0 2020-02-13 19:25 ./usr/lib/powerpc64le-linux-gnu/libhts.so.3 -> libhts.so.1.10.2 drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/share/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/share/doc/libhts3/ -rw-r--r-- root/root 1104 2020-02-13 19:25 ./usr/share/doc/libhts3/changelog.Debian.gz -rw-r--r-- root/root 5762 2019-09-04 08:27 ./usr/share/doc/libhts3/copyright tabix_1.10.2-2ubuntu2_ppc64el.deb --------------------------------- new debian package, version 2.0. size 407704 bytes: control archive=1128 bytes. 1055 bytes, 20 lines control 414 bytes, 7 lines md5sums Package: tabix Source: htslib Version: 1.10.2-2ubuntu2 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1779 Depends: libbz2-1.0, libc6 (>= 2.17), libcurl3-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), 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 2020-02-13 19:25 ./ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/bin/ -rwxr-xr-x root/root 198944 2020-02-13 19:25 ./usr/bin/bgzip -rwxr-xr-x root/root 788824 2020-02-13 19:25 ./usr/bin/htsfile -rwxr-xr-x root/root 788808 2020-02-13 19:25 ./usr/bin/tabix drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/share/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/share/doc/tabix/ -rw-r--r-- root/root 1104 2020-02-13 19:25 ./usr/share/doc/tabix/changelog.Debian.gz -rw-r--r-- root/root 5762 2019-09-04 08:27 ./usr/share/doc/tabix/copyright drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/share/man/ drwxr-xr-x root/root 0 2020-02-13 19:25 ./usr/share/man/man1/ lrwxrwxrwx root/root 0 2020-02-13 19:25 ./usr/share/man/man1/bgzip.1.gz -> tabix.1.gz -rw-r--r-- root/root 1919 2020-02-13 19:25 ./usr/share/man/man1/htsfile.1.gz -rw-r--r-- root/root 2831 2020-02-13 19:25 ./usr/share/man/man1/tabix.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build-Space: 72960 Build-Time: 325 Distribution: focal-proposed Host Architecture: ppc64el Install-Time: 11 Job: htslib_1.10.2-2ubuntu2.dsc Machine Architecture: ppc64el Package: htslib Package-Time: 336 Source-Version: 1.10.2-2ubuntu2 Space: 72960 Status: successful Version: 1.10.2-2ubuntu2 -------------------------------------------------------------------------------- Finished at 20200213-1942 Build needed 00:05:36, 72960k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=ppc64el PACKAGEBUILD-18704120 Scanning for processes to kill in build PACKAGEBUILD-18704120