https://launchpad.net/ubuntu/+source/samtools/1.19.2-1/+build/27788433
RUN: /usr/share/launchpad-buildd/bin/builder-prep 
Kernel version: Linux bos03-arm64-022 5.4.0-171-generic #189-Ubuntu SMP Fri Jan 5 14:23:34 UTC 2024 aarch64
Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1.
Syncing the system clock with the buildd NTP service...
18 Feb 05:18:01 ntpdate[2104]: adjust time server 10.211.37.1 offset 0.000945 sec
RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27788433 --image-type chroot /home/buildd/filecache-default/59612f0fc5bae33f6226b6e60c2e882b82c04bd0
Creating target for build PACKAGEBUILD-27788433
RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27788433
Starting target for build PACKAGEBUILD-27788433
RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27788433 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe'
Overriding sources.list in build-PACKAGEBUILD-27788433
RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27788433
Updating target for build PACKAGEBUILD-27788433
Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB]
Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB]
Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB]
Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
Get:5 http://ftpmaster.internal/ubuntu noble/main armhf Packages [1353 kB]
Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [519 kB]
Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf Packages [14.3 MB]
Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6029 kB]
Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [195 kB]
Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [70.6 kB]
Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [972 kB]
Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [408 kB]
Fetched 24.4 MB in 3s (7308 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:
  libperl5.36 libunistring2 perl-modules-5.36
Use 'sudo apt autoremove' to remove them.
The following NEW packages will be installed:
  cpp-13-arm-linux-gnueabihf cpp-arm-linux-gnueabihf
  g++-13-arm-linux-gnueabihf g++-arm-linux-gnueabihf
  gcc-13-arm-linux-gnueabihf gcc-14-base gcc-arm-linux-gnueabihf libperl5.38
  libunistring5 perl-modules-5.38
The following packages will be upgraded:
  apt apt-utils base-files base-passwd bash bash-completion binutils
  binutils-arm-linux-gnueabihf binutils-common bsdextrautils bsdutils
  ca-certificates coreutils cpp cpp-13 debconf debconf-i18n debianutils
  diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg
  gpg-agent gpgconf gpgv grep init init-system-helpers krb5-locales libacl1
  libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1
  libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6
  libc6-dev libcap-ng0 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12
  libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libfakeroot
  libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgdbm-compat4
  libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0
  libgssapi-krb5-2 libidn2-0 libip4tc2 libk5crypto3 libkeyutils1 libkmod2
  libkrb5-3 libkrb5support0 liblocale-gettext-perl liblzma5 libmd0 libmount1
  libncursesw6 libnsl-dev libnsl2 libp11-kit0 libpam-modules
  libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36
  libpng16-16 libproc2-0 libreadline8 libseccomp2 libselinux1
  libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1
  libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared
  libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6
  libtirpc-common libtirpc-dev libtirpc3 libubsan1 libudev1 libuuid1
  libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount
  ncurses-base ncurses-bin openssl optipng passwd perl perl-base
  perl-modules-5.36 pinentry-curses procps psmisc readline-common sed
  sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata
  ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g
151 upgraded, 10 newly installed, 0 to remove and 0 not upgraded.
Need to get 102 MB of archives.
After this operation, 46.6 MB of additional disk space will be used.
Get:1 http://ftpmaster.internal/ubuntu noble/main armhf libnsl-dev armhf 1.3.0-3 [65.8 kB]
Get:2 http://ftpmaster.internal/ubuntu noble/main armhf libcrypt-dev armhf 1:4.4.36-4 [136 kB]
Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6-dev armhf 2.39-0ubuntu1 [1352 kB]
Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-dev-bin armhf 2.39-0ubuntu1 [19.1 kB]
Get:5 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc-common all 1.3.4+ds-1build1 [8566 B]
Get:6 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc-dev armhf 1.3.4+ds-1build1 [207 kB]
Get:7 http://ftpmaster.internal/ubuntu noble/main armhf libgssapi-krb5-2 armhf 1.20.1-5build1 [118 kB]
Get:8 http://ftpmaster.internal/ubuntu noble/main armhf libkrb5-3 armhf 1.20.1-5build1 [320 kB]
Get:9 http://ftpmaster.internal/ubuntu noble/main armhf libk5crypto3 armhf 1.20.1-5build1 [78.6 kB]
Get:10 http://ftpmaster.internal/ubuntu noble/main armhf libkrb5support0 armhf 1.20.1-5build1 [31.3 kB]
Get:11 http://ftpmaster.internal/ubuntu noble/main armhf libkeyutils1 armhf 1.6.3-3 [8120 B]
Get:12 http://ftpmaster.internal/ubuntu noble/main armhf libssl3 armhf 3.0.10-1ubuntu4 [1553 kB]
Get:13 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc3 armhf 1.3.4+ds-1build1 [81.0 kB]
Get:14 http://ftpmaster.internal/ubuntu noble/main armhf libnsl2 armhf 1.3.0-3 [35.9 kB]
Get:15 http://ftpmaster.internal/ubuntu noble/main armhf libcrypt1 armhf 1:4.4.36-4 [104 kB]
Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-libc-dev armhf 6.8.0-11.11 [1553 kB]
Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6 armhf 2.39-0ubuntu1 [2830 kB]
Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-bin armhf 2.39-0ubuntu1 [528 kB]
Get:19 http://ftpmaster.internal/ubuntu noble/main armhf gcc-14-base armhf 14-20240201-3ubuntu1 [46.4 kB]
Get:20 http://ftpmaster.internal/ubuntu noble/main armhf libgcc-s1 armhf 14-20240201-3ubuntu1 [41.5 kB]
Get:21 http://ftpmaster.internal/ubuntu noble/main armhf base-files armhf 13ubuntu6 [84.0 kB]
Get:22 http://ftpmaster.internal/ubuntu noble/main armhf debianutils armhf 5.16 [93.1 kB]
Get:23 http://ftpmaster.internal/ubuntu noble/main armhf bash armhf 5.2.21-2ubuntu1 [673 kB]
Get:24 http://ftpmaster.internal/ubuntu noble/main armhf bsdutils armhf 1:2.39.2-6ubuntu1 [99.5 kB]
Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main armhf coreutils armhf 9.4-2ubuntu3 [1312 kB]
Get:26 http://ftpmaster.internal/ubuntu noble/main armhf diffutils armhf 1:3.10-1 [167 kB]
Get:27 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error-l10n all 1.47-3build1 [8024 B]
Get:28 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error0 armhf 1.47-3build1 [61.6 kB]
Get:29 http://ftpmaster.internal/ubuntu noble/main armhf libgcrypt20 armhf 1.10.3-2 [454 kB]
Get:30 http://ftpmaster.internal/ubuntu noble/main armhf liblzma5 armhf 5.4.5-0.3 [120 kB]
Get:31 http://ftpmaster.internal/ubuntu noble/main armhf libstdc++6 armhf 14-20240201-3ubuntu1 [714 kB]
Get:32 http://ftpmaster.internal/ubuntu noble/main armhf libacl1 armhf 2.3.1-4ubuntu1 [16.2 kB]
Get:33 http://ftpmaster.internal/ubuntu noble/main armhf libapparmor1 armhf 4.0.0~alpha4-0ubuntu1 [44.4 kB]
Get:34 http://ftpmaster.internal/ubuntu noble/main armhf libaudit-common all 1:3.1.2-2 [5594 B]
Get:35 http://ftpmaster.internal/ubuntu noble/main armhf libcap-ng0 armhf 0.8.4-2 [13.4 kB]
Get:36 http://ftpmaster.internal/ubuntu noble/main armhf libaudit1 armhf 1:3.1.2-2 [44.2 kB]
Get:37 http://ftpmaster.internal/ubuntu noble/main armhf libblkid1 armhf 2.39.2-6ubuntu1 [159 kB]
Get:38 http://ftpmaster.internal/ubuntu noble/main armhf libzstd1 armhf 1.5.5+dfsg2-2 [265 kB]
Get:39 http://ftpmaster.internal/ubuntu noble/main armhf libkmod2 armhf 30+20230601-2ubuntu1 [43.9 kB]
Get:40 http://ftpmaster.internal/ubuntu noble/main armhf libpcre2-8-0 armhf 10.42-4ubuntu1 [198 kB]
Get:41 http://ftpmaster.internal/ubuntu noble/main armhf libselinux1 armhf 3.5-2build1 [70.3 kB]
Get:42 http://ftpmaster.internal/ubuntu noble/main armhf libmount1 armhf 2.39.2-6ubuntu1 [171 kB]
Get:43 http://ftpmaster.internal/ubuntu noble/main armhf perl-modules-5.38 all 5.38.2-3 [3110 kB]
Get:44 http://ftpmaster.internal/ubuntu noble/main armhf libperl5.38 armhf 5.38.2-3 [4105 kB]
Get:45 http://ftpmaster.internal/ubuntu noble/main armhf perl armhf 5.38.2-3 [231 kB]
Get:46 http://ftpmaster.internal/ubuntu noble/main armhf perl-base armhf 5.38.2-3 [1670 kB]
Get:47 http://ftpmaster.internal/ubuntu noble/main armhf liblocale-gettext-perl armhf 1.07-6build1 [14.8 kB]
Get:48 http://ftpmaster.internal/ubuntu noble/main armhf libtext-iconv-perl armhf 1.7-8build1 [12.6 kB]
Get:49 http://ftpmaster.internal/ubuntu noble/main armhf libtext-charwidth-perl armhf 0.04-11build1 [8894 B]
Get:50 http://ftpmaster.internal/ubuntu noble/main armhf perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB]
Get:51 http://ftpmaster.internal/ubuntu noble/main armhf libperl5.36 armhf 5.36.0-10ubuntu1 [4019 kB]
Get:52 http://ftpmaster.internal/ubuntu noble/main armhf libdb5.3 armhf 5.3.28+dfsg2-4 [652 kB]
Get:53 http://ftpmaster.internal/ubuntu noble/main armhf libgdbm6 armhf 1.23-5 [29.8 kB]
Get:54 http://ftpmaster.internal/ubuntu noble/main armhf libgdbm-compat4 armhf 1.23-5 [5970 B]
Get:55 http://ftpmaster.internal/ubuntu noble/main armhf zlib1g armhf 1:1.3.dfsg-3ubuntu1 [50.6 kB]
Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main armhf debconf-i18n all 1.5.86 [205 kB]
Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf debconf all 1.5.86 [124 kB]
Get:58 http://ftpmaster.internal/ubuntu noble/main armhf libpam0g armhf 1.5.2-9.1ubuntu2 [60.2 kB]
Get:59 http://ftpmaster.internal/ubuntu noble/main armhf libseccomp2 armhf 2.5.5-1ubuntu1 [49.4 kB]
Get:60 http://ftpmaster.internal/ubuntu noble/main armhf systemd-sysv armhf 255.2-3ubuntu2 [11.9 kB]
Get:61 http://ftpmaster.internal/ubuntu noble/main armhf systemd-dev all 255.2-3ubuntu2 [101 kB]
Get:62 http://ftpmaster.internal/ubuntu noble/main armhf systemd armhf 255.2-3ubuntu2 [3495 kB]
Get:63 http://ftpmaster.internal/ubuntu noble/main armhf libsystemd-shared armhf 255.2-3ubuntu2 [2006 kB]
Get:64 http://ftpmaster.internal/ubuntu noble/main armhf libargon2-1 armhf 0~20190702+dfsg-4 [22.3 kB]
Get:65 http://ftpmaster.internal/ubuntu noble/main armhf libuuid1 armhf 2.39.2-6ubuntu1 [33.4 kB]
Get:66 http://ftpmaster.internal/ubuntu noble/main armhf libcryptsetup12 armhf 2:2.6.1-6ubuntu1 [216 kB]
Get:67 http://ftpmaster.internal/ubuntu noble/main armhf libfdisk1 armhf 2.39.2-6ubuntu1 [195 kB]
Get:68 http://ftpmaster.internal/ubuntu noble/main armhf mount armhf 2.39.2-6ubuntu1 [132 kB]
Get:69 http://ftpmaster.internal/ubuntu noble/main armhf libsystemd0 armhf 255.2-3ubuntu2 [408 kB]
Get:70 http://ftpmaster.internal/ubuntu noble/main armhf libudev1 armhf 255.2-3ubuntu2 [164 kB]
Get:71 http://ftpmaster.internal/ubuntu noble/main armhf libxxhash0 armhf 0.8.2-2 [31.3 kB]
Get:72 http://ftpmaster.internal/ubuntu noble/main armhf libapt-pkg6.0 armhf 2.7.11 [994 kB]
Get:73 http://ftpmaster.internal/ubuntu noble/main armhf tar armhf 1.35+dfsg-3 [236 kB]
Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg armhf 1.22.4ubuntu3 [1231 kB]
Get:75 http://ftpmaster.internal/ubuntu noble/main armhf grep armhf 3.11-4 [166 kB]
Get:76 http://ftpmaster.internal/ubuntu noble/main armhf login armhf 1:4.13+dfsg1-3ubuntu1 [200 kB]
Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ncurses-bin armhf 6.4+20240113-1ubuntu1 [178 kB]
Get:78 http://ftpmaster.internal/ubuntu noble/main armhf sed armhf 4.9-2 [198 kB]
Get:79 http://ftpmaster.internal/ubuntu noble/main armhf util-linux armhf 2.39.2-6ubuntu1 [1211 kB]
Get:80 http://ftpmaster.internal/ubuntu noble/main armhf libdebconfclient0 armhf 0.271ubuntu1 [10.8 kB]
Get:81 http://ftpmaster.internal/ubuntu noble/main armhf base-passwd armhf 3.6.3 [51.0 kB]
Get:82 http://ftpmaster.internal/ubuntu noble/main armhf init-system-helpers all 1.66ubuntu1 [39.4 kB]
Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB]
Get:84 http://ftpmaster.internal/ubuntu noble/main armhf sysvinit-utils armhf 3.08-3ubuntu1 [33.4 kB]
Get:85 http://ftpmaster.internal/ubuntu noble/main armhf apt armhf 2.7.11 [1363 kB]
Get:86 http://ftpmaster.internal/ubuntu noble/main armhf apt-utils armhf 2.7.11 [211 kB]
Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgv armhf 2.4.4-2ubuntu3 [223 kB]
Get:88 http://ftpmaster.internal/ubuntu noble/main armhf ubuntu-keyring all 2023.11.28.1 [11.1 kB]
Get:89 http://ftpmaster.internal/ubuntu noble/main armhf libffi8 armhf 3.4.4-2 [20.8 kB]
Get:90 http://ftpmaster.internal/ubuntu noble/main armhf libp11-kit0 armhf 0.25.3-4ubuntu1 [258 kB]
Get:91 http://ftpmaster.internal/ubuntu noble/main armhf libunistring5 armhf 1.1-2 [512 kB]
Get:92 http://ftpmaster.internal/ubuntu noble/main armhf libidn2-0 armhf 2.3.7-2 [96.1 kB]
Get:93 http://ftpmaster.internal/ubuntu noble/main armhf libgnutls30 armhf 3.8.3-1ubuntu1 [939 kB]
Get:94 http://ftpmaster.internal/ubuntu noble/main armhf libpam-modules-bin armhf 1.5.2-9.1ubuntu2 [43.6 kB]
Get:95 http://ftpmaster.internal/ubuntu noble/main armhf libpam-modules armhf 1.5.2-9.1ubuntu2 [265 kB]
Get:96 http://ftpmaster.internal/ubuntu noble/main armhf init armhf 1.66ubuntu1 [6186 B]
Get:97 http://ftpmaster.internal/ubuntu noble/main armhf libsmartcols1 armhf 2.39.2-6ubuntu1 [116 kB]
Get:98 http://ftpmaster.internal/ubuntu noble/main armhf uuid-runtime armhf 2.39.2-6ubuntu1 [40.7 kB]
Get:99 http://ftpmaster.internal/ubuntu noble/main armhf libattr1 armhf 1:2.5.2-1 [10.3 kB]
Get:100 http://ftpmaster.internal/ubuntu noble/main armhf libmd0 armhf 1.1.0-2 [23.1 kB]
Get:101 http://ftpmaster.internal/ubuntu noble/main armhf libpam-runtime all 1.5.2-9.1ubuntu2 [40.6 kB]
Get:102 http://ftpmaster.internal/ubuntu noble/main armhf libsemanage-common all 3.5-1build2 [10.0 kB]
Get:103 http://ftpmaster.internal/ubuntu noble/main armhf libsepol2 armhf 3.5-2 [262 kB]
Get:104 http://ftpmaster.internal/ubuntu noble/main armhf libsemanage2 armhf 3.5-1build2 [84.3 kB]
Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libncursesw6 armhf 6.4+20240113-1ubuntu1 [118 kB]
Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtinfo6 armhf 6.4+20240113-1ubuntu1 [90.5 kB]
Get:107 http://ftpmaster.internal/ubuntu noble/main armhf passwd armhf 1:4.13+dfsg1-3ubuntu1 [817 kB]
Get:108 http://ftpmaster.internal/ubuntu noble/main armhf g++-13 armhf 13.2.0-13ubuntu1 [14.0 kB]
Get:109 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13 armhf 13.2.0-13ubuntu1 [443 kB]
Get:110 http://ftpmaster.internal/ubuntu noble/main armhf cpp-13 armhf 13.2.0-13ubuntu1 [1032 B]
Get:111 http://ftpmaster.internal/ubuntu noble/main armhf cpp-13-arm-linux-gnueabihf armhf 13.2.0-13ubuntu1 [8754 kB]
Get:112 http://ftpmaster.internal/ubuntu noble/main armhf libcc1-0 armhf 14-20240201-3ubuntu1 [39.1 kB]
Get:113 http://ftpmaster.internal/ubuntu noble/main armhf libctf0 armhf 2.42-2ubuntu1 [87.6 kB]
Get:114 http://ftpmaster.internal/ubuntu noble/main armhf libctf-nobfd0 armhf 2.42-2ubuntu1 [87.7 kB]
Get:115 http://ftpmaster.internal/ubuntu noble/main armhf libsframe1 armhf 2.42-2ubuntu1 [12.8 kB]
Get:116 http://ftpmaster.internal/ubuntu noble/main armhf binutils-arm-linux-gnueabihf armhf 2.42-2ubuntu1 [2924 kB]
Get:117 http://ftpmaster.internal/ubuntu noble/main armhf libbinutils armhf 2.42-2ubuntu1 [460 kB]
Get:118 http://ftpmaster.internal/ubuntu noble/main armhf binutils armhf 2.42-2ubuntu1 [3080 B]
Get:119 http://ftpmaster.internal/ubuntu noble/main armhf binutils-common armhf 2.42-2ubuntu1 [216 kB]
Get:120 http://ftpmaster.internal/ubuntu noble/main armhf libstdc++-13-dev armhf 13.2.0-13ubuntu1 [2401 kB]
Get:121 http://ftpmaster.internal/ubuntu noble/main armhf libgomp1 armhf 14-20240201-3ubuntu1 [124 kB]
Get:122 http://ftpmaster.internal/ubuntu noble/main armhf libatomic1 armhf 14-20240201-3ubuntu1 [7802 B]
Get:123 http://ftpmaster.internal/ubuntu noble/main armhf libasan8 armhf 14-20240201-3ubuntu1 [2938 kB]
Get:124 http://ftpmaster.internal/ubuntu noble/main armhf libubsan1 armhf 14-20240201-3ubuntu1 [1151 kB]
Get:125 http://ftpmaster.internal/ubuntu noble/main armhf libgcc-13-dev armhf 13.2.0-13ubuntu1 [901 kB]
Get:126 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13-arm-linux-gnueabihf armhf 13.2.0-13ubuntu1 [16.8 MB]
Get:127 http://ftpmaster.internal/ubuntu noble/main armhf g++-13-arm-linux-gnueabihf armhf 13.2.0-13ubuntu1 [9933 kB]
Get:128 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13-base armhf 13.2.0-13ubuntu1 [46.6 kB]
Get:129 http://ftpmaster.internal/ubuntu noble/main armhf libproc2-0 armhf 2:4.0.4-2ubuntu1 [49.6 kB]
Get:130 http://ftpmaster.internal/ubuntu noble/main armhf mawk armhf 1.3.4.20240123-1 [115 kB]
Get:131 http://ftpmaster.internal/ubuntu noble/main armhf procps armhf 2:4.0.4-2ubuntu1 [699 kB]
Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main armhf sensible-utils all 0.0.22 [22.5 kB]
Get:133 http://ftpmaster.internal/ubuntu noble/main armhf openssl armhf 3.0.10-1ubuntu4 [973 kB]
Get:134 http://ftpmaster.internal/ubuntu noble/main armhf ca-certificates all 20240203 [159 kB]
Get:135 http://ftpmaster.internal/ubuntu noble/main armhf krb5-locales all 1.20.1-5build1 [13.7 kB]
Get:136 http://ftpmaster.internal/ubuntu noble/main armhf libip4tc2 armhf 1.8.10-3ubuntu1 [21.2 kB]
Get:137 http://ftpmaster.internal/ubuntu noble/main armhf readline-common all 8.2-3 [56.2 kB]
Get:138 http://ftpmaster.internal/ubuntu noble/main armhf libreadline8 armhf 8.2-3 [129 kB]
Get:139 http://ftpmaster.internal/ubuntu noble/main armhf libsqlite3-0 armhf 3.45.1-1 [590 kB]
Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main armhf tzdata all 2024a-1ubuntu1 [273 kB]
Get:141 http://ftpmaster.internal/ubuntu noble/main armhf bash-completion all 1:2.11-8 [180 kB]
Get:142 http://ftpmaster.internal/ubuntu noble/main armhf bsdextrautils armhf 2.39.2-6ubuntu1 [77.7 kB]
Get:143 http://ftpmaster.internal/ubuntu noble/main armhf libpng16-16 armhf 1.6.42-1 [166 kB]
Get:144 http://ftpmaster.internal/ubuntu noble/main armhf psmisc armhf 23.6-2 [176 kB]
Get:145 http://ftpmaster.internal/ubuntu noble/main armhf xz-utils armhf 5.4.5-0.3 [274 kB]
Get:146 http://ftpmaster.internal/ubuntu noble/main armhf g++ armhf 4:13.2.0-7ubuntu1 [1090 B]
Get:147 http://ftpmaster.internal/ubuntu noble/main armhf gcc armhf 4:13.2.0-7ubuntu1 [5022 B]
Get:148 http://ftpmaster.internal/ubuntu noble/main armhf cpp armhf 4:13.2.0-7ubuntu1 [22.4 kB]
Get:149 http://ftpmaster.internal/ubuntu noble/main armhf cpp-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [5320 B]
Get:150 http://ftpmaster.internal/ubuntu noble/main armhf gcc-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [1220 B]
Get:151 http://ftpmaster.internal/ubuntu noble/main armhf g++-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [966 B]
Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg-dev all 1.22.4ubuntu3 [1078 kB]
Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdpkg-perl all 1.22.4ubuntu3 [268 kB]
Get:154 http://ftpmaster.internal/ubuntu noble/main armhf lto-disabled-list all 46 [12.3 kB]
Get:155 http://ftpmaster.internal/ubuntu noble/main armhf libfakeroot armhf 1.33-1 [28.7 kB]
Get:156 http://ftpmaster.internal/ubuntu noble/main armhf fakeroot armhf 1.33-1 [68.6 kB]
Get:157 http://ftpmaster.internal/ubuntu noble/main armhf pinentry-curses armhf 1.2.1-3ubuntu1 [36.4 kB]
Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg armhf 2.4.4-2ubuntu3 [523 kB]
Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgconf armhf 2.4.4-2ubuntu3 [115 kB]
Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-agent armhf 2.4.4-2ubuntu3 [236 kB]
Get:161 http://ftpmaster.internal/ubuntu noble/main armhf optipng armhf 0.7.8+ds-1 [109 kB]
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Current default time zone: 'Etc/UTC'
Local time is now:      Sun Feb 18 05:18:44 UTC 2024.
Universal Time is now:  Sun Feb 18 05:18:44 UTC 2024.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

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rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL
14 added, 5 removed; done.
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Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27788433 armhf noble-proposed -c chroot:build-PACKAGEBUILD-27788433 --arch=armhf --dist=noble-proposed --nolog samtools_1.19.2-1.dsc
Initiating build PACKAGEBUILD-27788433 with 4 jobs across 4 processor cores.
Kernel reported to sbuild: 5.4.0-171-generic #189-Ubuntu SMP Fri Jan 5 14:23:34 UTC 2024 armv7l
sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos03-arm64-022.buildd

+==============================================================================+
| samtools 1.19.2-1 (armhf)                    Sun, 18 Feb 2024 05:18:52 +0000 |
+==============================================================================+

Package: samtools
Version: 1.19.2-1
Source Version: 1.19.2-1
Distribution: noble-proposed
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any

I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27788433/chroot-autobuild' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/samtools-jGfY9E/resolver-rL4zmk' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Local sources
-------------

samtools_1.19.2-1.dsc exists in .; copying to chroot
I: NOTICE: Log filtering will replace 'build/samtools-jGfY9E/samtools-1.19.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/samtools-jGfY9E' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [459 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [534 B]
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Reading package lists...
Reading package lists...

Install main 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:
  apt-utils ca-certificates debconf-i18n krb5-locales libgpg-error-l10n
  libgpm2 libip4tc2 liblocale-gettext-perl libnss-nis libnss-nisplus
  libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl
  libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf autoconf-archive automake autopoint autotools-dev debhelper
  debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext
  gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1
  libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
  libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl
  libhts-dev libhts3 libhtscodecs2 libicu74 libio-pty-perl libldap2
  liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses6 libnghttp2-14
  libpipeline1 libpkgconf3 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db
  libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkgconf
  pkgconf-bin po-debconf tabix zlib1g-dev
Suggested packages:
  gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev
  libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev
  libldap2-dev librtmp-dev libssh2-1-dev liblzma-doc ncurses-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 libldap-common
  publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf autoconf-archive automake autopoint autotools-dev debhelper
  debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext
  gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1
  libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
  libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl
  libhts-dev libhts3 libhtscodecs2 libicu74 libio-pty-perl libldap2
  liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses6 libnghttp2-14
  libpipeline1 libpkgconf3 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db
  libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkgconf
  pkgconf-bin po-debconf sbuild-build-depends-main-dummy tabix zlib1g-dev
0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded.
Need to get 24.9 MB of archives.
After this operation, 85.5 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [754 B]
Get:2 http://ftpmaster.internal/ubuntu noble/universe armhf autoconf-archive all 20220903-3 [681 kB]
Get:3 http://ftpmaster.internal/ubuntu noble/main armhf libelf1 armhf 0.190-1 [49.8 kB]
Get:4 http://ftpmaster.internal/ubuntu noble/main armhf libicu74 armhf 74.2-1ubuntu1 [10.5 MB]
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Get:6 http://ftpmaster.internal/ubuntu noble/main armhf libmagic-mgc armhf 1:5.45-2 [307 kB]
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Get:8 http://ftpmaster.internal/ubuntu noble/main armhf file armhf 1:5.45-2 [21.1 kB]
Get:9 http://ftpmaster.internal/ubuntu noble/main armhf gettext-base armhf 0.21-14ubuntu1 [38.0 kB]
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Get:11 http://ftpmaster.internal/ubuntu noble/main armhf groff-base armhf 1.23.0-3 [948 kB]
Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libncurses6 armhf 6.4+20240113-1ubuntu1 [88.1 kB]
Get:13 http://ftpmaster.internal/ubuntu noble/main armhf libnghttp2-14 armhf 1.59.0-1 [68.1 kB]
Get:14 http://ftpmaster.internal/ubuntu noble/main armhf libpipeline1 armhf 1.5.7-1 [26.2 kB]
Get:15 http://ftpmaster.internal/ubuntu noble/main armhf libpsl5 armhf 0.21.2-1build1 [55.5 kB]
Get:16 http://ftpmaster.internal/ubuntu noble/main armhf man-db armhf 2.12.0-3 [1196 kB]
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Get:26 http://ftpmaster.internal/ubuntu noble/main armhf libsub-override-perl all 0.10-1 [10.0 kB]
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Get:30 http://ftpmaster.internal/ubuntu noble/main armhf debugedit armhf 1:5.0-5 [42.8 kB]
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Get:34 http://ftpmaster.internal/ubuntu noble/main armhf po-debconf all 1.0.21+nmu1 [233 kB]
Get:35 http://ftpmaster.internal/ubuntu noble/main armhf debhelper all 13.13ubuntu1 [868 kB]
Get:36 http://ftpmaster.internal/ubuntu noble/main armhf libbrotli1 armhf 1.1.0-2 [318 kB]
Get:37 http://ftpmaster.internal/ubuntu noble/main armhf libbz2-dev armhf 1.0.8-5build1 [29.8 kB]
Get:38 http://ftpmaster.internal/ubuntu noble/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-4 [19.0 kB]
Get:39 http://ftpmaster.internal/ubuntu noble/main armhf libsasl2-2 armhf 2.1.28+dfsg1-4 [49.8 kB]
Get:40 http://ftpmaster.internal/ubuntu noble/main armhf libldap2 armhf 2.6.7+dfsg-1~exp1ubuntu1 [170 kB]
Get:41 http://ftpmaster.internal/ubuntu noble/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build4 [52.8 kB]
Get:42 http://ftpmaster.internal/ubuntu noble/main armhf libssh-4 armhf 0.10.6-2 [190 kB]
Get:43 http://ftpmaster.internal/ubuntu noble/main armhf libcurl3-gnutls armhf 8.5.0-2ubuntu2 [289 kB]
Get:44 http://ftpmaster.internal/ubuntu noble/main armhf libcurl4-gnutls-dev armhf 8.5.0-2ubuntu2 [407 kB]
Get:45 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate0 armhf 1.19-1 [41.3 kB]
Get:46 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate-dev armhf 1.19-1 [48.4 kB]
Get:47 http://ftpmaster.internal/ubuntu noble/universe armhf libhtscodecs2 armhf 1.6.0-1 [65.9 kB]
Get:48 http://ftpmaster.internal/ubuntu noble/universe armhf libhts3 armhf 1.18+ds-1 [385 kB]
Get:49 http://ftpmaster.internal/ubuntu noble/main armhf liblzma-dev armhf 5.4.5-0.3 [189 kB]
Get:50 http://ftpmaster.internal/ubuntu noble/main armhf zlib1g-dev armhf 1:1.3.dfsg-3ubuntu1 [882 kB]
Get:51 http://ftpmaster.internal/ubuntu noble/universe armhf libhts-dev armhf 1.18+ds-1 [1709 kB]
Get:52 http://ftpmaster.internal/ubuntu noble/main armhf libio-pty-perl armhf 1:1.20-1 [30.8 kB]
Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libncurses-dev armhf 6.4+20240113-1ubuntu1 [501 kB]
Get:54 http://ftpmaster.internal/ubuntu noble/main armhf libpkgconf3 armhf 1.8.1-2 [26.3 kB]
Get:55 http://ftpmaster.internal/ubuntu noble/main armhf pkgconf-bin armhf 1.8.1-2 [20.6 kB]
Get:56 http://ftpmaster.internal/ubuntu noble/main armhf pkgconf armhf 1.8.1-2 [16.7 kB]
Get:57 http://ftpmaster.internal/ubuntu noble/universe armhf tabix armhf 1.18+ds-1 [421 kB]
Preconfiguring packages ...
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Setting up liblzma-dev:armhf (5.4.5-0.3) ...
Setting up libicu74:armhf (74.2-1ubuntu1) ...
Setting up zlib1g-dev:armhf (1:1.3.dfsg-3ubuntu1) ...
Setting up libuchardet0:armhf (0.0.8-1) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up libdeflate-dev:armhf (1.19-1) ...
Setting up tabix (1.18+ds-1) ...
Setting up libelf1:armhf (0.190-1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3ubuntu1) ...
Setting up libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu1) ...
Setting up libbz2-dev:armhf (1.0.8-5build1) ...
Setting up automake (1:1.16.5-1.3ubuntu1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up libdw1:armhf (0.190-1) ...
Setting up libncurses-dev:armhf (6.4+20240113-1ubuntu1) ...
Setting up gettext (0.21-14ubuntu1) ...
Setting up libtool (2.4.7-7) ...
Setting up libcurl3-gnutls:armhf (8.5.0-2ubuntu2) ...
Setting up libcurl4-gnutls-dev:armhf (8.5.0-2ubuntu2) ...
Setting up pkgconf:armhf (1.8.1-2) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
Setting up debugedit (1:5.0-5) ...
Setting up libhts3:armhf (1.18+ds-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.18+ds-1) ...
Setting up man-db (2.12.0-3) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer.
Setting up debhelper (13.13ubuntu1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.39-0ubuntu1) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any all)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 5.4.0-171-generic #189-Ubuntu SMP Fri Jan 5 14:23:34 UTC 2024 arm64 (armv7l)
Toolchain package versions: binutils_2.42-2ubuntu1 dpkg-dev_1.22.4ubuntu3 g++-13_13.2.0-13ubuntu1 gcc-13_13.2.0-13ubuntu1 libc6-dev_2.39-0ubuntu1 libstdc++-13-dev_13.2.0-13ubuntu1 libstdc++6_14-20240201-3ubuntu1 linux-libc-dev_6.8.0-11.11
Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.11 apt-utils_2.7.11 autoconf_2.71-3 autoconf-archive_20220903-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu6 base-passwd_3.6.3 bash_5.2.21-2ubuntu1 bash-completion_1:2.11-8 binutils_2.42-2ubuntu1 binutils-arm-linux-gnueabihf_2.42-2ubuntu1 binutils-common_2.42-2ubuntu1 bsdextrautils_2.39.2-6ubuntu1 bsdutils_1:2.39.2-6ubuntu1 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20240203 coreutils_9.4-2ubuntu3 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-13ubuntu1 cpp-13-arm-linux-gnueabihf_13.2.0-13ubuntu1 cpp-arm-linux-gnueabihf_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu1 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.13ubuntu1 debianutils_5.16 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.4ubuntu3 dpkg-dev_1.22.4ubuntu3 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.33-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-13ubuntu1 g++-13-arm-linux-gnueabihf_13.2.0-13ubuntu1 g++-arm-linux-gnueabihf_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-13ubuntu1 gcc-13-arm-linux-gnueabihf_13.2.0-13ubuntu1 gcc-13-base_13.2.0-13ubuntu1 gcc-14-base_14-20240201-3ubuntu1 gcc-arm-linux-gnueabihf_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu1 gettext-base_0.21-14ubuntu1 gpg_2.4.4-2ubuntu3 gpg-agent_2.4.4-2ubuntu3 gpgconf_2.4.4-2ubuntu3 gpgv_2.4.4-2ubuntu3 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1ubuntu1 hostname_3.23+nmu1ubuntu1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-5build1 libacl1_2.3.1-4ubuntu1 libapparmor1_4.0.0~alpha4-0ubuntu1 libapt-pkg6.0_2.7.11 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_14-20240201-3ubuntu1 libassuan0_2.5.6-1 libatomic1_14-20240201-3ubuntu1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2 libaudit1_1:3.1.2-2 libbinutils_2.42-2ubuntu1 libblkid1_2.39.2-6ubuntu1 libbrotli1_1.1.0-2 libbz2-1.0_1.0.8-5build1 libbz2-dev_1.0.8-5build1 libc-bin_2.39-0ubuntu1 libc-dev-bin_2.39-0ubuntu1 libc6_2.39-0ubuntu1 libc6-dev_2.39-0ubuntu1 libcap-ng0_0.8.4-2 libcap2_1:2.66-4ubuntu1 libcc1-0_14-20240201-3ubuntu1 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.6.1-6ubuntu1 libctf-nobfd0_2.42-2ubuntu1 libctf0_2.42-2ubuntu1 libcurl3-gnutls_8.5.0-2ubuntu2 libcurl4-gnutls-dev_8.5.0-2ubuntu2 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271ubuntu1 libdebhelper-perl_13.13ubuntu1 libdeflate-dev_1.19-1 libdeflate0_1.19-1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.22.4ubuntu3 libdw1_0.190-1 libelf1_0.190-1 libext2fs2_1.47.0-2ubuntu1 libfakeroot_1.33-1 libfdisk1_2.39.2-6ubuntu1 libffi8_3.4.4-2 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-13ubuntu1 libgcc-s1_14-20240201-3ubuntu1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30_3.8.3-1ubuntu1 libgomp1_14-20240201-3ubuntu1 libgpg-error-l10n_1.47-3build1 libgpg-error0_1.47-3build1 libgpm2_1.20.7-10build1 libgssapi-krb5-2_1.20.1-5build1 libhogweed6_3.9.1-2 libhts-dev_1.18+ds-1 libhts3_1.18+ds-1 libhtscodecs2_1.6.0-1 libicu74_74.2-1ubuntu1 libidn2-0_2.3.7-2 libio-pty-perl_1:1.20-1 libip4tc2_1.8.10-3ubuntu1 libisl23_0.26-3 libjansson4_2.14-2 libjson-c5_0.17-1 libk5crypto3_1.20.1-5build1 libkeyutils1_1.6.3-3 libkmod2_30+20230601-2ubuntu1 libkrb5-3_1.20.1-5build1 libkrb5support0_1.20.1-5build1 libldap2_2.6.7+dfsg-1~exp1ubuntu1 liblocale-gettext-perl_1.07-6build1 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblz4-1_1.9.4-1 liblzma-dev_5.4.5-0.3 liblzma5_5.4.5-0.3 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-2 libmount1_2.39.2-6ubuntu1 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncurses-dev_6.4+20240113-1ubuntu1 libncurses6_6.4+20240113-1ubuntu1 libncursesw6_6.4+20240113-1ubuntu1 libnettle8_3.9.1-2 libnghttp2-14_1.59.0-1 libnpth0_1.6-3build2 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-0ubuntu6 libp11-kit0_0.25.3-4ubuntu1 libpam-modules_1.5.2-9.1ubuntu2 libpam-modules-bin_1.5.2-9.1ubuntu2 libpam-runtime_1.5.2-9.1ubuntu2 libpam0g_1.5.2-9.1ubuntu2 libpcre2-8-0_10.42-4ubuntu1 libperl5.36_5.36.0-10ubuntu1 libperl5.38_5.38.2-3 libpipeline1_1.5.7-1 libpkgconf3_1.8.1-2 libpng16-16_1.6.42-1 libproc2-0_2:4.0.4-2ubuntu1 libpsl5_0.21.2-1build1 libreadline8_8.2-3 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.5-1ubuntu1 libselinux1_3.5-2build1 libsemanage-common_3.5-1build2 libsemanage2_3.5-1build2 libsepol2_3.5-2 libsframe1_2.42-2ubuntu1 libsmartcols1_2.39.2-6ubuntu1 libsqlite3-0_3.45.1-1 libss2_1.47.0-2ubuntu1 libssh-4_0.10.6-2 libssl3_3.0.10-1ubuntu4 libstdc++-13-dev_13.2.0-13ubuntu1 libstdc++6_14-20240201-3ubuntu1 libsub-override-perl_0.10-1 libsystemd-shared_255.2-3ubuntu2 libsystemd0_255.2-3ubuntu2 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11build1 libtext-iconv-perl_1.7-8build1 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20240113-1ubuntu1 libtirpc-common_1.3.4+ds-1build1 libtirpc-dev_1.3.4+ds-1build1 libtirpc3_1.3.4+ds-1build1 libtool_2.4.7-7 libubsan1_14-20240201-3ubuntu1 libuchardet0_0.0.8-1 libudev1_255.2-3ubuntu2 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-6ubuntu1 libxml2_2.9.14+dfsg-1.3ubuntu1 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.0-11.11 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-3ubuntu1 logsave_1.47.0-2ubuntu1 lto-disabled-list_46 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-3 mawk_1.3.4.20240123-1 mount_2.39.2-6ubuntu1 ncurses-base_6.4+20240113-1ubuntu1 ncurses-bin_6.4+20240113-1ubuntu1 openssl_3.0.10-1ubuntu4 optipng_0.7.8+ds-1 passwd_1:4.13+dfsg1-3ubuntu1 patch_2.7.6-7build2 perl_5.38.2-3 perl-base_5.38.2-3 perl-modules-5.36_5.36.0-10ubuntu1 perl-modules-5.38_5.38.2-3 pinentry-curses_1.2.1-3ubuntu1 pkgbinarymangler_154 pkgconf_1.8.1-2 pkgconf-bin_1.8.1-2 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-2ubuntu1 psmisc_23.6-2 readline-common_8.2-3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 systemd_255.2-3ubuntu2 systemd-dev_255.2-3ubuntu2 systemd-sysv_255.2-3ubuntu2 sysvinit-utils_3.08-3ubuntu1 tabix_1.18+ds-1 tar_1.35+dfsg-3 tzdata_2024a-1ubuntu1 ubuntu-keyring_2023.11.28.1 usrmerge_35ubuntu1 util-linux_2.39.2-6ubuntu1 uuid-runtime_2.39.2-6ubuntu1 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3ubuntu1 zlib1g-dev_1:1.3.dfsg-3ubuntu1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: samtools
Binary: samtools, samtools-test
Architecture: any all
Version: 1.19.2-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>, Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://www.htslib.org/
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/samtools
Vcs-Git: https://salsa.debian.org/med-team/samtools.git
Testsuite: autopkgtest
Testsuite-Triggers: tabix
Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl <!nocheck>, libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev
Package-List:
 samtools deb science optional arch=any
 samtools-test deb science optional arch=all
Checksums-Sha1:
 8dff98a03e9295730b24e26cb1447b41887af669 5666279 samtools_1.19.2.orig.tar.gz
 ac8048d48e8883df9b4700dd4a26bccd6542cfc8 21752 samtools_1.19.2-1.debian.tar.xz
Checksums-Sha256:
 93b4ee042003d536a2f822a17dd5e65439f724214d5d2b5becc8a9f190ef2efd 5666279 samtools_1.19.2.orig.tar.gz
 ab11a07d6e8e80fadb62672ec5974867a0328f31d5b6faa7c2d8e5b7de9936a1 21752 samtools_1.19.2-1.debian.tar.xz
Files:
 dc7d1649a27689287499876dc05785c4 5666279 samtools_1.19.2.orig.tar.gz
 3eea35b7ce97c48454c4f5b378ab722a 21752 samtools_1.19.2-1.debian.tar.xz

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gpgv: Signature made Sat Feb 17 17:32:01 2024 UTC
gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv:                issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./samtools_1.19.2-1.dsc: no acceptable signature found
dpkg-source: info: extracting samtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking samtools_1.19.2.orig.tar.gz
dpkg-source: info: unpacking samtools_1.19.2-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying reproducible.patch

Check disk 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-27788433
SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27788433
SCHROOT_COMMAND=env
SCHROOT_GID=2501
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=build-PACKAGEBUILD-27788433
SCHROOT_UID=2001
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=unknown
USER=buildd
V=1

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon <buildd@bos03-arm64-022.buildd> -B -rfakeroot
dpkg-buildpackage: info: source package samtools
dpkg-buildpackage: info: source version 1.19.2-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from samtools-1.19.2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f config.mk
touch config.mk
dh_auto_clean --
	make -j4 distclean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam*
cd test/reference && rm -f mpileup.*.fai
rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o
rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
rm -rf autom4te.cache
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_clean
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/samtools.substvars debian/samtools-test.substvars debian/files
	rm -fr -- debian/samtools/ debian/tmp/ debian/samtools-test/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
 debian/rules binary-arch
dh binary-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
configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals
./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
	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 '/<<PKGBUILDDIR>>'
touch config.mk
aclocal --force -I debian/ -I /usr/share/aclocal
autoconf
configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals
./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
dh_auto_configure -- --with-htslib=system
	./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
checking for gawk... no
checking for mawk... mawk
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for Curses library... yes
checking for working curses.h... yes
checking for X/Open Enhanced Curses conformance... no
checking for Curses color functions... yes
checking for obsolete Curses functions... yes
checking for library containing cbreak... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
	rm -f debian/samtools.debhelper.log
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- \
  CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
  CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
  LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
	make -j4 "CFLAGS=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=3" "LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_aux.o bam_aux.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_index.o bam_index.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_plcmd.o bam_plcmd.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam_view.o sam_view.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_fastq.o bam_fastq.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_cat.o bam_cat.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_md.o bam_md.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_plbuf.o bam_plbuf.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_reheader.o bam_reheader.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_sort.o bam_sort.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_rmdup.o bam_rmdup.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_rmdupse.o bam_rmdupse.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_mate.o bam_mate.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_stat.o bam_stat.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_color.o bam_color.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
echo '#define SAMTOOLS_VERSION "1.19.2"' > version.h
echo '#define SAMTOOLS_CC "gcc"' >> version.h
echo '#define SAMTOOLS_CPPFLAGS "-frelease  -Wdate-time -D_FORTIFY_SOURCE=3"' >> version.h
echo '#define SAMTOOLS_CFLAGS "-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1"' >> version.h
echo '#define SAMTOOLS_LDFLAGS "-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now"' >> version.h
echo '#define SAMTOOLS_HTSDIR ""' >> version.h
echo '#define SAMTOOLS_LIBS ""' >> version.h
echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h
sed -i -e 's@/<<PKGBUILDDIR>>@«BUILDPATH»@g' version.h
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam2bcf.o bam2bcf.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sample.o sample.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cut_target.o cut_target.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o phase.o phase.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam2depth.o bam2depth.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o coverage.o coverage.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o padding.o padding.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bedcov.o bedcov.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bamshuf.o bamshuf.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o faidx.o faidx.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o dict.o dict.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o stats.o stats.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o stats_isize.o stats_isize.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_flags.o bam_flags.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_split.o bam_split.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_tview.o bam_tview.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_tview_curses.o bam_tview_curses.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_tview_html.o bam_tview_html.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_lpileup.o bam_lpileup.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_quickcheck.o bam_quickcheck.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_addrprg.o bam_addrprg.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_markdup.o bam_markdup.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tmp_file.o tmp_file.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_ampliconclip.o bam_ampliconclip.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o amplicon_stats.o amplicon_stats.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_import.o bam_import.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_samples.o bam_samples.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam_consensus.o bam_consensus.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o consensus_pileup.o consensus_pileup.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o reference.o reference.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o reset.o reset.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram_size.o cram_size.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o lz4/lz4.o lz4/lz4.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam_opts.o sam_opts.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam_utils.o sam_utils.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bedidx.o bedidx.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bam.o bam.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o misc/ace2sam.o misc/ace2sam.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -DMAQ_LONGREADS -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o misc/maq2sam-long.o misc/maq2sam.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o misc/maq2sam-short.o misc/maq2sam.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o misc/md5fa.o misc/md5fa.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o misc/wgsim.o misc/wgsim.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test.o test/test.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/vcf-miniview.o test/vcf-miniview.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fno-stack-clash-protection -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/samtools-1.19.2-1 -I.  -I./lz4 -frelease  -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bamtk.o bamtk.c
cc1: warning: command-line option ‘-frelease’ is valid for D but not for C
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o
gcc  -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz 
gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz 
gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz 
gcc  -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz 
gcc  -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz 
gcc  -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz 
gcc  -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz  -lpthread
gcc  -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz  -lpthread
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
	rm -f debian/samtools.debhelper.log
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test -- BGZIP=/usr/bin/bgzip
	make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/<<PKGBUILDDIR>>'
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
test/split/test_parse_args
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-}
test_reference:
	/<<PKGBUILDDIR>>/samtools reference test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/<<PKGBUILDDIR>>/samtools reference -e test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/<<PKGBUILDDIR>>/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/<<PKGBUILDDIR>>/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/<<PKGBUILDDIR>>/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/<<PKGBUILDDIR>>/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/<<PKGBUILDDIR>>/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/<<PKGBUILDDIR>>/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram
.. ok

/usr/bin/bgzip -c -b 65272 -s 5 /tmp/kS2G4yOY52/bgzip.dat.gz
.. ok

/usr/bin/bgzip -c -b 979200 -s 6 /tmp/kS2G4yOY52/bgzip.dat.gz
.. ok

/usr/bin/bgzip -c -b 652804 -s 6 /tmp/kS2G4yOY52/bgzip.dat.gz
.. ok

/<<PKGBUILDDIR>>/samtools faidx /tmp/kS2G4yOY52/faidx.fa 3:11-13 | grep -v '^>'
.. ok

/<<PKGBUILDDIR>>/samtools faidx /tmp/kS2G4yOY52/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok

/<<PKGBUILDDIR>>/samtools faidx /tmp/kS2G4yOY52/faidx.fa 2:998-1003 | grep -v '^>'
.. ok

/<<PKGBUILDDIR>>/samtools faidx /tmp/kS2G4yOY52/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok

/<<PKGBUILDDIR>>/samtools faidx /tmp/kS2G4yOY52/faidx.fa 1:100-104 | grep -v '^>'
.. ok

/<<PKGBUILDDIR>>/samtools faidx /tmp/kS2G4yOY52/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok

/<<PKGBUILDDIR>>/samtools faidx /tmp/kS2G4yOY52/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok

/<<PKGBUILDDIR>>/samtools faidx /tmp/kS2G4yOY52/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok

/<<PKGBUILDDIR>>/samtools fqidx /tmp/kS2G4yOY52/fqidx.fq 3:11-13
.. ok

.. ok

/<<PKGBUILDDIR>>/samtools fqidx /tmp/kS2G4yOY52/fqidx.fq.gz 3:11-13
.. ok

.. ok

/<<PKGBUILDDIR>>/samtools fqidx /tmp/kS2G4yOY52/fqidx.fq 2:998-1003
.. ok

.. ok

/<<PKGBUILDDIR>>/samtools fqidx /tmp/kS2G4yOY52/fqidx.fq.gz 2:998-1003
.. ok

.. ok

/<<PKGBUILDDIR>>/samtools fqidx /tmp/kS2G4yOY52/fqidx.fq 1:100-104
.. ok

.. ok

/<<PKGBUILDDIR>>/samtools fqidx /tmp/kS2G4yOY52/fqidx.fq.gz 1:100-104
.. ok

.. ok

/<<PKGBUILDDIR>>/samtools fqidx /tmp/kS2G4yOY52/fqidx.fq 1:99998-100007
.. ok

.. ok

/<<PKGBUILDDIR>>/samtools fqidx /tmp/kS2G4yOY52/fqidx.fq.gz 1:99998-100007
.. ok

.. ok

test_dict:
	/<<PKGBUILDDIR>>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /<<PKGBUILDDIR>>/test/dat/dict.fa
.. ok

test_dict:
	/<<PKGBUILDDIR>>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/kS2G4yOY52/dict.fa.gz
.. ok

test_dict:
	cat /<<PKGBUILDDIR>>/test/dat/dict.fa | /<<PKGBUILDDIR>>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz
.. ok

test_dict:
	/<<PKGBUILDDIR>>/samtools dict -AH < /<<PKGBUILDDIR>>/test/dat/dict.alias.fa
.. ok

test_dict:
	/<<PKGBUILDDIR>>/samtools dict -H -l /<<PKGBUILDDIR>>/test/dat/dict.alt < /<<PKGBUILDDIR>>/test/dat/dict.alias.fa
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools view /tmp/kS2G4yOY52/large_chrom.bam ref2
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools view /tmp/kS2G4yOY52/large_chrom.bam ref2:1-541556283
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools index /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam && cat /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools view -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/kS2G4yOY52/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools view -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/kS2G4yOY52/test_input_1_b.bam.bai
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools merge -O sam - -X -cp -R ref2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai /tmp/kS2G4yOY52/test_input_1_b.bam.bai
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools view -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/kS2G4yOY52/test_input_1_b_opt.bam.bai ref2
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools index /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools index -M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam && cat /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools view -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools index -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam /tmp/kS2G4yOY52/auto_indexed.csi && cat /tmp/kS2G4yOY52/auto_indexed.csi
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools index /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.cram /tmp/kS2G4yOY52/auto_indexed.crai && cat /tmp/kS2G4yOY52/auto_indexed.crai
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools index -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.sam /tmp/kS2G4yOY52/auto_indexed.csi && cat /tmp/kS2G4yOY52/auto_indexed.csi
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/kS2G4yOY52/large_chrom.bam ref2
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/kS2G4yOY52/large_chrom.bam ref2:1-541556283
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools index -@ 2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam && cat /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools view -@ 2 -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/kS2G4yOY52/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools view -@ 2 -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/kS2G4yOY52/test_input_1_b.bam.bai
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 -O sam - -X -cp -R ref2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai /tmp/kS2G4yOY52/test_input_1_b.bam.bai
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools view -@ 2 -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/kS2G4yOY52/test_input_1_b_opt.bam.bai ref2
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools index -@ 2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools index -@ 2 -M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam && cat /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools view -@ 2 -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools index -@ 2 -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam /tmp/kS2G4yOY52/auto_indexed.csi && cat /tmp/kS2G4yOY52/auto_indexed.csi
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools index -@ 2 /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.cram /tmp/kS2G4yOY52/auto_indexed.crai && cat /tmp/kS2G4yOY52/auto_indexed.crai
.. ok

test_index:
	/<<PKGBUILDDIR>>/samtools index -@ 2 -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.sam /tmp/kS2G4yOY52/auto_indexed.csi && cat /tmp/kS2G4yOY52/auto_indexed.csi
.. ok

test_mpileup:
	/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/kS2G4yOY52/mpileup.bam.list -f /tmp/kS2G4yOY52/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/kS2G4yOY52/mpileup.cram.list -f /tmp/kS2G4yOY52/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/kS2G4yOY52/mpileup.bam.urllist -f /tmp/kS2G4yOY52/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/kS2G4yOY52/mpileup.cram.urllist -f /tmp/kS2G4yOY52/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/kS2G4yOY52/mpileup.ref.fa.gz -r17:1050-1060 /tmp/kS2G4yOY52/mpileup.1.bam | grep -v mpileup
.. ok

test_mpileup:
	/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/kS2G4yOY52/mpileup.ref.fa.gz -r17:1050-1060 /tmp/kS2G4yOY52/mpileup.1.cram | grep -v mpileup
.. ok

test_mpileup:
	/<<PKGBUILDDIR>>/samtools mpileup /<<PKGBUILDDIR>>/test/mpileup/overlap.bam | grep 128814202
.. ok

test_usage:
	samtools
	samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, consensus, merge, mpileup, sort, split, quickcheck, fastq, fasta, import, reference, reset, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, head, tview, view, depad, samples, help, version
.. ok

test_usage_subcommand:
	samtools dict

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools faidx
.. ok

test_usage_subcommand:
	samtools fqidx
.. ok

test_usage_subcommand:
	samtools index
.. ok

test_usage_subcommand:
	samtools calmd

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools fixmate
.. ok

test_usage_subcommand:
	samtools reheader

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools targetcut

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools addreplacerg
.. ok

test_usage_subcommand:
	samtools markdup

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools ampliconclip

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools collate
.. ok

test_usage_subcommand:
	samtools cat

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools consensus
.. ok

test_usage_subcommand:
	samtools merge
.. ok

test_usage_subcommand:
	samtools mpileup

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools sort
.. ok

test_usage_subcommand:
	samtools split
.. ok

test_usage_subcommand:
	samtools quickcheck
.. ok

test_usage_subcommand:
	samtools fastq
.. ok

test_usage_subcommand:
	samtools fasta
.. ok

test_usage_subcommand:
	samtools import
.. ok

test_usage_subcommand:
	samtools reference
.. ok

test_usage_subcommand:
	samtools reset
.. ok

test_usage_subcommand:
	samtools bedcov

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools coverage
.. ok

test_usage_subcommand:
	samtools depth
.. ok

test_usage_subcommand:
	samtools flagstat
.. ok

test_usage_subcommand:
	samtools idxstats
.. ok

test_usage_subcommand:
	samtools phase

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools stats
.. ok

test_usage_subcommand:
	samtools ampliconstats
.. ok

test_usage_subcommand:
	samtools flags
.. ok

test_usage_subcommand:
	samtools head
.. ok

test_usage_subcommand:
	samtools tview

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools view
.. ok

test_usage_subcommand:
	samtools depad

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools samples

	Usage on stderr rather than stdout
.. expected failure

test_view:
	Generating test data file .................. done
	1: SAM -> BAM -> SAM                                        .. ok

	2: SAM -> uncompressed BAM                                  .. ok

	3: uncompressed BAM -> SAM and compare                      .. ok

	4: SAM -> fast compressed BAM                               .. ok

	5: fast compressed BAM -> SAM and compare                   .. ok

	6: SAM -> CRAM -> SAM (UR header tags)                      .. ok

	7: SAM -> CRAM -> SAM (M5 header tags)                      .. ok

	8: BAM -> CRAM with UR -> SAM                               .. ok

	9: SAM -> BAM (M5 header tags)                              .. ok

	10: SAM -> BAM -> CRAM -> SAM (M5 header tags)              .. ok

	11: CRAM -> BAM with UR                                     .. ok

	12: CRAM -> BAM with M5                                     .. ok

	13: SAM -> SAM via stdout                                   .. ok

	14: SAM -> BAM via stdout                                   .. ok

	15: SAM -> CRAM via stdout                                  .. ok

	16: SAM from stdin -> SAM                                   .. ok

	17: BAM from stdin -> SAM                                   .. ok

	18: CRAM from stdin -> SAM                                  .. ok

	19: samtools view -H (SAM input)                            .. ok

	20: samtools view -H (BAM input)                            .. ok

	21: samtools view -H (CRAM input)                           .. ok

	22: No headers (SAM input)                                  .. ok

	23: No headers (BAM input)                                  .. ok

	24: No headers (CRAM input)                                 .. ok

	25: Filter -f 128 (SAM input)                               .. ok

	26: Count -f 128 (SAM input)                                .. ok

	27: Filter -f 128 (BAM input)                               .. ok

	28: Count -f 128 (BAM input)                                .. ok

	29: Filter -f 128 (CRAM input)                              .. ok

	30: Count -f 128 (CRAM input)                               .. ok

	31: Filter -F 128 (SAM input)                               .. ok

	32: Count -F 128 (SAM input)                                .. ok

	33: Filter -F 128 (BAM input)                               .. ok

	34: Count -F 128 (BAM input)                                .. ok

	35: Filter -F 128 (CRAM input)                              .. ok

	36: Count -F 128 (CRAM input)                               .. ok

	37: Filter -F 128 -f 2 (SAM input)                          .. ok

	38: Count -F 128 -f 2 (SAM input)                           .. ok

	39: Filter -F 128 -f 2 (BAM input)                          .. ok

	40: Count -F 128 -f 2 (BAM input)                           .. ok

	41: Filter -F 128 -f 2 (CRAM input)                         .. ok

	42: Count -F 128 -f 2 (CRAM input)                          .. ok

	43: Filter -r grp2 (SAM input)                              .. ok

	44: Count -r grp2 (SAM input)                               .. ok

	45: Filter -r grp2 (BAM input)                              .. ok

	46: Count -r grp2 (BAM input)                               .. ok

	47: Filter -r grp2 (CRAM input)                             .. ok

	48: Count -r grp2 (CRAM input)                              .. ok

	49: Filter -R /tmp/kS2G4yOY52/view.001.fogn (SAM input)     .. ok

	50: Count -R /tmp/kS2G4yOY52/view.001.fogn (SAM input)      .. ok

	51: Filter -R /tmp/kS2G4yOY52/view.001.fogn (BAM input)     .. ok

	52: Count -R /tmp/kS2G4yOY52/view.001.fogn (BAM input)      .. ok

	53: Filter -R /tmp/kS2G4yOY52/view.001.fogn (CRAM input)    .. ok

	54: Count -R /tmp/kS2G4yOY52/view.001.fogn (CRAM input)     .. ok

	55: Filter -R /tmp/kS2G4yOY52/view.001.fogn -r grp2 (SAM input).. ok

	56: Count -R /tmp/kS2G4yOY52/view.001.fogn -r grp2 (SAM input).. ok

	57: Filter -R /tmp/kS2G4yOY52/view.001.fogn -r grp2 (BAM input).. ok

	58: Count -R /tmp/kS2G4yOY52/view.001.fogn -r grp2 (BAM input).. ok

	59: Filter -R /tmp/kS2G4yOY52/view.001.fogn -r grp2 (CRAM input).. ok

	60: Count -R /tmp/kS2G4yOY52/view.001.fogn -r grp2 (CRAM input).. ok

	61: Filter -r grp2 -R /tmp/kS2G4yOY52/view.001.fogn (SAM input).. ok

	62: Count -r grp2 -R /tmp/kS2G4yOY52/view.001.fogn (SAM input).. ok

	63: Filter -r grp2 -R /tmp/kS2G4yOY52/view.001.fogn (BAM input).. ok

	64: Count -r grp2 -R /tmp/kS2G4yOY52/view.001.fogn (BAM input).. ok

	65: Filter -r grp2 -R /tmp/kS2G4yOY52/view.001.fogn (CRAM input).. ok

	66: Count -r grp2 -R /tmp/kS2G4yOY52/view.001.fogn (CRAM input).. ok

	67: Filter -N /tmp/kS2G4yOY52/view.001.forn (SAM input)     .. ok

	68: Count -N /tmp/kS2G4yOY52/view.001.forn (SAM input)      .. ok

	69: Filter -N /tmp/kS2G4yOY52/view.001.forn (BAM input)     .. ok

	70: Count -N /tmp/kS2G4yOY52/view.001.forn (BAM input)      .. ok

	71: Filter -N /tmp/kS2G4yOY52/view.001.forn (CRAM input)    .. ok

	72: Count -N /tmp/kS2G4yOY52/view.001.forn (CRAM input)     .. ok

	73: Filter -d BC (SAM input)                                .. ok

	74: Count -d BC (SAM input)                                 .. ok

	75: Filter -d BC (BAM input)                                .. ok

	76: Count -d BC (BAM input)                                 .. ok

	77: Filter -d BC (CRAM input)                               .. ok

	78: Count -d BC (CRAM input)                                .. ok

	79: Filter -d BC:TGCA (SAM input)                           .. ok

	80: Count -d BC:TGCA (SAM input)                            .. ok

	81: Filter -d BC:TGCA (BAM input)                           .. ok

	82: Count -d BC:TGCA (BAM input)                            .. ok

	83: Filter -d BC:TGCA (CRAM input)                          .. ok

	84: Count -d BC:TGCA (CRAM input)                           .. ok

	85: Filter -D BC:/tmp/kS2G4yOY52/view.001.fobc (SAM input)  .. ok

	86: Count -D BC:/tmp/kS2G4yOY52/view.001.fobc (SAM input)   .. ok

	87: Filter -D BC:/tmp/kS2G4yOY52/view.001.fobc (BAM input)  .. ok

	88: Count -D BC:/tmp/kS2G4yOY52/view.001.fobc (BAM input)   .. ok

	89: Filter -D BC:/tmp/kS2G4yOY52/view.001.fobc (CRAM input) .. ok

	90: Count -D BC:/tmp/kS2G4yOY52/view.001.fobc (CRAM input)  .. ok

	91: Filter -D BC:/tmp/kS2G4yOY52/view.001.fobc -d BC:TGCA (SAM input).. ok

	92: Count -D BC:/tmp/kS2G4yOY52/view.001.fobc -d BC:TGCA (SAM input).. ok

	93: Filter -D BC:/tmp/kS2G4yOY52/view.001.fobc -d BC:TGCA (BAM input).. ok

	94: Count -D BC:/tmp/kS2G4yOY52/view.001.fobc -d BC:TGCA (BAM input).. ok

	95: Filter -D BC:/tmp/kS2G4yOY52/view.001.fobc -d BC:TGCA (CRAM input).. ok

	96: Count -D BC:/tmp/kS2G4yOY52/view.001.fobc -d BC:TGCA (CRAM input).. ok

	97: Filter -d BC:TGCA -D BC:/tmp/kS2G4yOY52/view.001.fobc (SAM input).. ok

	98: Count -d BC:TGCA -D BC:/tmp/kS2G4yOY52/view.001.fobc (SAM input).. ok

	99: Filter -d BC:TGCA -D BC:/tmp/kS2G4yOY52/view.001.fobc (BAM input).. ok

	100: Count -d BC:TGCA -D BC:/tmp/kS2G4yOY52/view.001.fobc (BAM input).. ok

	101: Filter -d BC:TGCA -D BC:/tmp/kS2G4yOY52/view.001.fobc (CRAM input).. ok

	102: Count -d BC:TGCA -D BC:/tmp/kS2G4yOY52/view.001.fobc (CRAM input).. ok

	103: Filter -D RG:/tmp/kS2G4yOY52/view.001.fogn (SAM input) .. ok

	104: Count -D RG:/tmp/kS2G4yOY52/view.001.fogn (SAM input)  .. ok

	105: Filter -D RG:/tmp/kS2G4yOY52/view.001.fogn (BAM input) .. ok

	106: Count -D RG:/tmp/kS2G4yOY52/view.001.fogn (BAM input)  .. ok

	107: Filter -D RG:/tmp/kS2G4yOY52/view.001.fogn (CRAM input).. ok

	108: Count -D RG:/tmp/kS2G4yOY52/view.001.fogn (CRAM input) .. ok

	109: Filter -d NE:TGCA (SAM input)                          .. ok

	110: Count -d NE:TGCA (SAM input)                           .. ok

	111: Filter -d NE:TGCA (BAM input)                          .. ok

	112: Count -d NE:TGCA (BAM input)                           .. ok

	113: Filter -d NE:TGCA (CRAM input)                         .. ok

	114: Count -d NE:TGCA (CRAM input)                          .. ok

	115: Filter -d TGCA (SAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -o /tmp/kS2G4yOY52/view.test115.sam -h -d TGCA /tmp/kS2G4yOY52/view.001.sam --no-PG


.. expected failure

	116: Count -d TGCA (SAM input)                              samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -c -d TGCA /tmp/kS2G4yOY52/view.001.sam --no-PG


.. expected failure

	117: Filter -d TGCA (BAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -o /tmp/kS2G4yOY52/view.test117.sam -h -d TGCA /tmp/kS2G4yOY52/view.test001.bam --no-PG


.. expected failure

	118: Count -d TGCA (BAM input)                              samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -c -d TGCA /tmp/kS2G4yOY52/view.test001.bam --no-PG


.. expected failure

	119: Filter -d TGCA (CRAM input)                            samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -o /tmp/kS2G4yOY52/view.test119.sam -h -d TGCA /tmp/kS2G4yOY52/view.test006.cram --no-PG


.. expected failure

	120: Count -d TGCA (CRAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -c -d TGCA /tmp/kS2G4yOY52/view.test006.cram --no-PG


.. expected failure

	121: Filter -D BClong:/tmp/kS2G4yOY52/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/kS2G4yOY52/view.001.fobc"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -o /tmp/kS2G4yOY52/view.test121.sam -h -D BClong:/tmp/kS2G4yOY52/view.001.fobc /tmp/kS2G4yOY52/view.001.sam --no-PG


.. expected failure

	122: Count -D BClong:/tmp/kS2G4yOY52/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/kS2G4yOY52/view.001.fobc"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/kS2G4yOY52/view.001.fobc /tmp/kS2G4yOY52/view.001.sam --no-PG


.. expected failure

	123: Filter -D BClong:/tmp/kS2G4yOY52/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/kS2G4yOY52/view.001.fobc"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -o /tmp/kS2G4yOY52/view.test123.sam -h -D BClong:/tmp/kS2G4yOY52/view.001.fobc /tmp/kS2G4yOY52/view.test001.bam --no-PG


.. expected failure

	124: Count -D BClong:/tmp/kS2G4yOY52/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/kS2G4yOY52/view.001.fobc"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/kS2G4yOY52/view.001.fobc /tmp/kS2G4yOY52/view.test001.bam --no-PG


.. expected failure

	125: Filter -D BClong:/tmp/kS2G4yOY52/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/kS2G4yOY52/view.001.fobc"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -o /tmp/kS2G4yOY52/view.test125.sam -h -D BClong:/tmp/kS2G4yOY52/view.001.fobc /tmp/kS2G4yOY52/view.test006.cram --no-PG


.. expected failure

	126: Count -D BClong:/tmp/kS2G4yOY52/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/kS2G4yOY52/view.001.fobc"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/kS2G4yOY52/view.001.fobc /tmp/kS2G4yOY52/view.test006.cram --no-PG


.. expected failure

	127: Filter -d BC:ACGT -d RG:grp2 (SAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -o /tmp/kS2G4yOY52/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/kS2G4yOY52/view.001.sam --no-PG


.. expected failure

	128: Count -d BC:ACGT -d RG:grp2 (SAM input)                samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/kS2G4yOY52/view.001.sam --no-PG


.. expected failure

	129: Filter -d BC:ACGT -d RG:grp2 (BAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -o /tmp/kS2G4yOY52/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/kS2G4yOY52/view.test001.bam --no-PG


.. expected failure

	130: Count -d BC:ACGT -d RG:grp2 (BAM input)                samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/kS2G4yOY52/view.test001.bam --no-PG


.. expected failure

	131: Filter -d BC:ACGT -d RG:grp2 (CRAM input)              samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -o /tmp/kS2G4yOY52/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/kS2G4yOY52/view.test006.cram --no-PG


.. expected failure

	132: Count -d BC:ACGT -d RG:grp2 (CRAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/<<PKGBUILDDIR>>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/kS2G4yOY52/view.test006.cram --no-PG


.. expected failure

	133: Filter -d NM:13 (SAM input)                            .. ok

	134: Count -d NM:13 (SAM input)                             .. ok

	135: Filter -d NM:13 (BAM input)                            .. ok

	136: Count -d NM:13 (BAM input)                             .. ok

	137: Filter -d NM:13 (CRAM input)                           .. ok

	138: Count -d NM:13 (CRAM input)                            .. ok

	139: Filter -d ab:z (SAM input)                             .. ok

	140: Count -d ab:z (SAM input)                              .. ok

	141: Filter -d ab:z (BAM input)                             .. ok

	142: Count -d ab:z (BAM input)                              .. ok

	143: Filter -d ab:z (CRAM input)                            .. ok

	144: Count -d ab:z (CRAM input)                             .. ok

	145: Filter -l Library 2 (SAM input)                        .. ok

	146: Count -l Library 2 (SAM input)                         .. ok

	147: Filter -l Library 2 (BAM input)                        .. ok

	148: Count -l Library 2 (BAM input)                         .. ok

	149: Filter -l Library 2 (CRAM input)                       .. ok

	150: Count -l Library 2 (CRAM input)                        .. ok

	151: Filter -l Library 3 (SAM input)                        .. ok

	152: Count -l Library 3 (SAM input)                         .. ok

	153: Filter -l Library 3 (BAM input)                        .. ok

	154: Count -l Library 3 (BAM input)                         .. ok

	155: Filter -l Library 3 (CRAM input)                       .. ok

	156: Count -l Library 3 (CRAM input)                        .. ok

	157: Filter -q 50 (SAM input)                               .. ok

	158: Count -q 50 (SAM input)                                .. ok

	159: Filter -q 50 (BAM input)                               .. ok

	160: Count -q 50 (BAM input)                                .. ok

	161: Filter -q 50 (CRAM input)                              .. ok

	162: Count -q 50 (CRAM input)                               .. ok

	163: Filter -q 99 (SAM input)                               .. ok

	164: Count -q 99 (SAM input)                                .. ok

	165: Filter -q 99 (BAM input)                               .. ok

	166: Count -q 99 (BAM input)                                .. ok

	167: Filter -q 99 (CRAM input)                              .. ok

	168: Count -q 99 (CRAM input)                               .. ok

	169: Filter -q 100 (SAM input)                              .. ok

	170: Count -q 100 (SAM input)                               .. ok

	171: Filter -q 100 (BAM input)                              .. ok

	172: Count -q 100 (BAM input)                               .. ok

	173: Filter -q 100 (CRAM input)                             .. ok

	174: Count -q 100 (CRAM input)                              .. ok

	175: Filter -x fa (SAM input)                               .. ok

	176: Count -x fa (SAM input)                                .. ok

	177: Filter -x fa (BAM input)                               .. ok

	178: Count -x fa (BAM input)                                .. ok

	179: Filter -x fa (CRAM input)                              .. ok

	180: Count -x fa (CRAM input)                               .. ok

	181: Filter -x fa -x ha (SAM input)                         .. ok

	182: Count -x fa -x ha (SAM input)                          .. ok

	183: Filter -x fa -x ha (BAM input)                         .. ok

	184: Count -x fa -x ha (BAM input)                          .. ok

	185: Filter -x fa -x ha (CRAM input)                        .. ok

	186: Count -x fa -x ha (CRAM input)                         .. ok

	187: Filter -x fa,ha (SAM input)                            .. ok

	188: Count -x fa,ha (SAM input)                             .. ok

	189: Filter -x fa,ha (BAM input)                            .. ok

	190: Count -x fa,ha (BAM input)                             .. ok

	191: Filter -x fa,ha (CRAM input)                           .. ok

	192: Count -x fa,ha (CRAM input)                            .. ok

	193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	205: Filter -x fa -r grp2 (SAM input)                       .. ok

	206: Count -x fa -r grp2 (SAM input)                        .. ok

	207: Filter -x fa -r grp2 (BAM input)                       .. ok

	208: Count -x fa -r grp2 (BAM input)                        .. ok

	209: Filter -x fa -r grp2 (CRAM input)                      .. ok

	210: Count -x fa -r grp2 (CRAM input)                       .. ok

	211: Filter -x RG -r grp2 (SAM input)                       .. ok

	212: Count -x RG -r grp2 (SAM input)                        .. ok

	213: Filter -x RG -r grp2 (BAM input)                       .. ok

	214: Count -x RG -r grp2 (BAM input)                        .. ok

	215: Filter -x RG -r grp2 (CRAM input)                      .. ok

	216: Count -x RG -r grp2 (CRAM input)                       .. ok

	217: Filter -m 10 (SAM input)                               .. ok

	218: Count -m 10 (SAM input)                                .. ok

	219: Filter -m 10 (BAM input)                               .. ok

	220: Count -m 10 (BAM input)                                .. ok

	221: Filter -m 10 (CRAM input)                              .. ok

	222: Count -m 10 (CRAM input)                               .. ok

	223: Filter -m 11 (SAM input)                               .. ok

	224: Count -m 11 (SAM input)                                .. ok

	225: Filter -m 11 (BAM input)                               .. ok

	226: Count -m 11 (BAM input)                                .. ok

	227: Filter -m 11 (CRAM input)                              .. ok

	228: Count -m 11 (CRAM input)                               .. ok

	229: Filter -m 15 (SAM input)                               .. ok

	230: Count -m 15 (SAM input)                                .. ok

	231: Filter -m 15 (BAM input)                               .. ok

	232: Count -m 15 (BAM input)                                .. ok

	233: Filter -m 15 (CRAM input)                              .. ok

	234: Count -m 15 (CRAM input)                               .. ok

	235: Filter -m 16 (SAM input)                               .. ok

	236: Count -m 16 (SAM input)                                .. ok

	237: Filter -m 16 (BAM input)                               .. ok

	238: Count -m 16 (BAM input)                                .. ok

	239: Filter -m 16 (CRAM input)                              .. ok

	240: Count -m 16 (CRAM input)                               .. ok

	241: Filter -e !(flag & 128) && (flag & 2) (SAM input)      .. ok

	242: Count -e !(flag & 128) && (flag & 2) (SAM input)       .. ok

	243: Filter -e !(flag & 128) && (flag & 2) (BAM input)      .. ok

	244: Count -e !(flag & 128) && (flag & 2) (BAM input)       .. ok

	245: Filter -e !(flag & 128) && (flag & 2) (CRAM input)     .. ok

	246: Count -e !(flag & 128) && (flag & 2) (CRAM input)      .. ok

	247: Filter -e [BC] (SAM input)                             .. ok

	248: Count -e [BC] (SAM input)                              .. ok

	249: Filter -e [BC] (BAM input)                             .. ok

	250: Count -e [BC] (BAM input)                              .. ok

	251: Filter -e [BC] (CRAM input)                            .. ok

	252: Count -e [BC] (CRAM input)                             .. ok

	253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok

	254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok

	255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok

	256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok

	257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok

	258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok

	259: Filter -e mapq >= 50 (SAM input)                       .. ok

	260: Count -e mapq >= 50 (SAM input)                        .. ok

	261: Filter -e mapq >= 50 (BAM input)                       .. ok

	262: Count -e mapq >= 50 (BAM input)                        .. ok

	263: Filter -e mapq >= 50 (CRAM input)                      .. ok

	264: Count -e mapq >= 50 (CRAM input)                       .. ok

	265: Filter -e mapq >= 99 (SAM input)                       .. ok

	266: Count -e mapq >= 99 (SAM input)                        .. ok

	267: Filter -e mapq >= 99 (BAM input)                       .. ok

	268: Count -e mapq >= 99 (BAM input)                        .. ok

	269: Filter -e mapq >= 99 (CRAM input)                      .. ok

	270: Count -e mapq >= 99 (CRAM input)                       .. ok

	271: Filter -e mapq >= 100 (SAM input)                      .. ok

	272: Count -e mapq >= 100 (SAM input)                       .. ok

	273: Filter -e mapq >= 100 (BAM input)                      .. ok

	274: Count -e mapq >= 100 (BAM input)                       .. ok

	275: Filter -e mapq >= 100 (CRAM input)                     .. ok

	276: Count -e mapq >= 100 (CRAM input)                      .. ok

	277: 1bp reads file SAM -> BAM -> SAM                       .. ok

	278: 1bp reads file SAM -> CRAM -> SAM                      .. ok

	278: Region  Z (BAM input)                                  .. ok

	279: Count  Z (BAM input)                                   .. ok

	280: Region  Z (CRAM input)                                 .. ok

	281: Count  Z (CRAM input)                                  .. ok

	282: Region  Z:30 (BAM input)                               .. ok

	283: Count  Z:30 (BAM input)                                .. ok

	284: Region  Z:30 (CRAM input)                              .. ok

	285: Count  Z:30 (CRAM input)                               .. ok

	286: Region  Z:20-40 (BAM input)                            .. ok

	287: Count  Z:20-40 (BAM input)                             .. ok

	288: Region  Z:20-40 (CRAM input)                           .. ok

	289: Count  Z:20-40 (CRAM input)                            .. ok

	290: Region  ref1 (BAM input)                               .. ok

	291: Count  ref1 (BAM input)                                .. ok

	292: Region  ref1 (CRAM input)                              .. ok

	293: Count  ref1 (CRAM input)                               .. ok

	294: Region  ref1:15 (BAM input)                            .. ok

	295: Count  ref1:15 (BAM input)                             .. ok

	296: Region  ref1:15 (CRAM input)                           .. ok

	297: Count  ref1:15 (CRAM input)                            .. ok

	298: Region  ref1:15-45 (BAM input)                         .. ok

	299: Count  ref1:15-45 (BAM input)                          .. ok

	300: Region  ref1:15-45 (CRAM input)                        .. ok

	301: Count  ref1:15-45 (CRAM input)                         .. ok

	302: Region  ref1:15-45 ref2 (BAM input)                    .. ok

	303: Count  ref1:15-45 ref2 (BAM input)                     .. ok

	304: Region  ref1:15-45 ref2 (CRAM input)                   .. ok

	305: Count  ref1:15-45 ref2 (CRAM input)                    .. ok

	306: Region  ref1:15-45 ref2:16 (BAM input)                 .. ok

	307: Count  ref1:15-45 ref2:16 (BAM input)                  .. ok

	308: Region  ref1:15-45 ref2:16 (CRAM input)                .. ok

	309: Count  ref1:15-45 ref2:16 (CRAM input)                 .. ok

	310: Region  ref1:15-45 ref2:16-31 (BAM input)              .. ok

	311: Count  ref1:15-45 ref2:16-31 (BAM input)               .. ok

	312: Region  ref1:15-45 ref2:16-31 (CRAM input)             .. ok

	313: Count  ref1:15-45 ref2:16-31 (CRAM input)              .. ok

	314: Region  ref1:15-15 ref1:45-45 (BAM input)              .. ok

	315: Count  ref1:15-15 ref1:45-45 (BAM input)               .. ok

	316: Region  ref1:15-15 ref1:45-45 (CRAM input)             .. ok

	317: Count  ref1:15-15 ref1:45-45 (CRAM input)              .. ok

	318: Region -f 128 ref1 (BAM input)                         .. ok

	319: Count -f 128 ref1 (BAM input)                          .. ok

	320: Region -f 128 ref1 (CRAM input)                        .. ok

	321: Count -f 128 ref1 (CRAM input)                         .. ok

	322: Region -q 50 ref1:15-45 (BAM input)                    .. ok

	323: Count -q 50 ref1:15-45 (BAM input)                     .. ok

	324: Region -q 50 ref1:15-45 (CRAM input)                   .. ok

	325: Count -q 50 ref1:15-45 (CRAM input)                    .. ok

	326: Region -r grp2 ref1:15-45 (BAM input)                  .. ok

	327: Count -r grp2 ref1:15-45 (BAM input)                   .. ok

	328: Region -r grp2 ref1:15-45 (CRAM input)                 .. ok

	329: Count -r grp2 ref1:15-45 (CRAM input)                  .. ok

	330: Region  * (BAM input)                                  .. ok

	331: Count  * (BAM input)                                   .. ok

	332: Region  * (CRAM input)                                 .. ok

	333: Count  * (CRAM input)                                  .. ok

	334: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed  (BAM input).. ok

	335: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed  (BAM input).. ok

	336: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed  (CRAM input).. ok

	337: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed  (CRAM input).. ok

	338: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed  (BAM input).. ok

	339: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed  (BAM input).. ok

	340: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed  (CRAM input).. ok

	341: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed  (CRAM input).. ok

	342: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed  (BAM input).. ok

	343: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed  (BAM input).. ok

	344: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed  (CRAM input).. ok

	345: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed  (CRAM input).. ok

	346: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed  (BAM input).. ok

	347: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed  (BAM input).. ok

	348: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed  (CRAM input).. ok

	349: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed  (CRAM input).. ok

	350: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.03.bed  (BAM input).. ok

	351: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.03.bed  (BAM input).. ok

	352: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.03.bed  (CRAM input).. ok

	353: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.03.bed  (CRAM input).. ok

	354: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok

	355: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok

	356: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok

	357: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok

	358: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok

	359: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok

	360: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok

	361: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok

	362: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok

	363: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok

	364: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok

	365: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok

	366: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok

	367: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok

	368: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok

	369: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok

	370: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok

	371: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok

	372: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok

	373: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok

	374: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok

	375: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok

	376: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok

	377: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok

	378: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok

	379: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok

	380: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok

	381: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok

	382: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1  (BAM input).. ok

	383: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1  (BAM input).. ok

	384: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1  (CRAM input).. ok

	385: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1  (CRAM input).. ok

	386: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128  (BAM input).. ok

	387: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128  (BAM input).. ok

	388: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128  (CRAM input).. ok

	389: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128  (CRAM input).. ok

	390: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5  (BAM input).. ok

	391: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5  (BAM input).. ok

	392: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5  (CRAM input).. ok

	393: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5  (CRAM input).. ok

	394: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok

	395: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok

	396: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok

	397: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok

	398: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap  (BAM input).. ok

	399: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap  (BAM input).. ok

	400: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap  (CRAM input).. ok

	401: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap  (CRAM input).. ok

	402: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok

	403: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok

	404: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok

	405: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok

	406: Make BAM with no M5/UR tags                            .. ok

	407: Add @SQ with -t (SAM -> SAM)                           .. ok

	408: Add @SQ with -T (SAM -> SAM)                           .. ok

	409: Add @SQ with -t (BAM -> SAM)                           .. ok

	410: Add @SQ with -T (BAM -> SAM)                           .. ok

	411: Add @SQ with -t (SAM -> BAM)                           .. ok

	412: Add @SQ with -T (SAM -> BAM)                           .. ok

	413: Add @SQ with -t (BAM -> BAM)                           .. ok

	414: Add @SQ with -T (BAM -> BAM)                           .. ok

	415: Add @SQ with -t (SAM -> CRAM)                          .. ok

	416: Add @SQ with -T (SAM -> CRAM)                          .. ok

	417: Add @SQ with -t (BAM -> CRAM)                          .. ok

	418: Add @SQ with -T (BAM -> CRAM)                          .. ok

	419: Make CRAM with no UR field                             .. ok

	420: Decoding CRAM with no UR field via -T                  .. ok

	421: CIGAR B-operator removal                               .. ok

	422: Big SAM -> BAM                                         .. ok

	423: Big SAM -> BAM (2 threads)                             .. ok

	424: Big SAM -> BAM (4 threads)                             .. ok

	425: Big SAM -> CRAM                                        .. ok

	426: Big SAM -> CRAM (2 threads)                            .. ok

	427: Big SAM -> CRAM (4 threads)                            .. ok

	428: Subsample 0.2 (SAM input) ............ ok

	429: Subsample 0.5 (SAM input) ............ ok

	430: Subsample 0.8 (SAM input) ............ ok

	431: Subsample 0.2 (BAM input) ............ ok

	432: Subsample 0.5 (BAM input) ............ ok

	433: Subsample 0.8 (BAM input) ............ ok

	434: Subsample 0.2 (CRAM input) ............ ok

	435: Subsample 0.5 (CRAM input) ............ ok

	436: Subsample 0.8 (CRAM input) ............ ok

	437: SAM add PG                                             .. ok

	438: Unset dup flag, remove dt and do tags                  .. ok

	439: Unmap dup flagged reads.                               .. ok

	440: Unmap dup flagged reads.                               .. ok

	441: fetch pairs                                            .. ok

	442: fetch pairs                                            .. ok

	443: fetch pairs                                            .. ok

test_head:
	/<<PKGBUILDDIR>>/samtools head /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok

test_head:
	/<<PKGBUILDDIR>>/samtools head -h 0 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok

test_head:
	/<<PKGBUILDDIR>>/samtools head -h 1 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok

test_head:
	/<<PKGBUILDDIR>>/samtools head -h 5 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok

test_head:
	/<<PKGBUILDDIR>>/samtools head -h 29 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok

test_head:
	/<<PKGBUILDDIR>>/samtools head -h 30 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok

test_head:
	/<<PKGBUILDDIR>>/samtools head -n 0 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok

test_head:
	/<<PKGBUILDDIR>>/samtools head -n 1 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok

test_head:
	/<<PKGBUILDDIR>>/samtools head -n 5 /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok

test_head:
	/<<PKGBUILDDIR>>/samtools head -h 5 -n 5 < /<<PKGBUILDDIR>>/test/dat/view.001.sam
.. ok

test_cat:
	Generating test data file .................. done
	Generate BAM file #1                                        .. ok

	Generate CRAM file #1                                       .. ok

	Generating test data file .................. done
	Generate BAM file #2                                        .. ok

	Generate CRAM file #2                                       .. ok

	Generating test data file .................. done
	Generate BAM file #3                                        .. ok

	Generate CRAM file #3                                       .. ok

	Generating test data file .................. done
	Generate BAM file #4                                        .. ok

	Generate CRAM file #4                                       .. ok

	1: cat BAM files                                            .. ok

	2: cat recompressed BAM files                               .. ok

	3: cat CRAM files                                           .. ok

	4: cat BAM files to stdout                                  .. ok

	5: cat recompressed BAM files to stdout                     .. ok

	6: cat CRAM files to stdout                                 .. ok

	7: cat BAM files with new header                            .. ok

	8: cat recompressed BAM files with new header               .. ok

	9: cat CRAM files with new header                           .. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import -0 test/bam2fq/1.1.fq.expected  | /<<PKGBUILDDIR>>/samtools fastq -0 /<<PKGBUILDDIR>>/test/0.fq
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import -s test/bam2fq/1.1.fq.expected  | /<<PKGBUILDDIR>>/samtools fastq -0 /<<PKGBUILDDIR>>/test/0.fq
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import -s test/bam2fq/5.s.fq.expected  | /<<PKGBUILDDIR>>/samtools fastq -s /<<PKGBUILDDIR>>/test/s.fq
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /<<PKGBUILDDIR>>/samtools fastq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /<<PKGBUILDDIR>>/samtools fastq -N -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /<<PKGBUILDDIR>>/samtools fastq -i --index-format 'i*i*' -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /<<PKGBUILDDIR>>/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /<<PKGBUILDDIR>>/samtools fastq -N -T RG,BC,QT -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /<<PKGBUILDDIR>>/samtools fastq -N -T RG,BC,QT,MD,ia -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG	ID:rgid'
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import test/import/2.interleaved.fq -T ""
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import test/import/3.interleaved.fq -i
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import test/import/4.aux.fq -T "*"
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import test/import/4.aux.fq -T ""
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import test/import/4.aux.fq -T XZ,XA,AA
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import --i1 test/import/5-i1.fq --i2  test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq
.. ok

test_import:
	/<<PKGBUILDDIR>>/samtools import --i1 test/import/5-i1.fq --i2  test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ
.. ok

test_bam2fq:
	Generate BAM file                                           .. ok

	Generate CRAM file                                          .. ok

	1: fastq  (SAM input)                                       [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	2: fastq -n (SAM input)                                     [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	3: fastq  (BAM input)                                       [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	4: fastq -n (BAM input)                                     [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	5: fastq  (CRAM input)                                      [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	6: fastq -n (CRAM input)                                    [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.002.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.003.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  --barcode-tag BC --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  --barcode-tag BC -O --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  --barcode-tag BC -O --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.010.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  --barcode-tag BC -N --index-format 'n*i*' --i1 /<<PKGBUILDDIR>>/test/bc_split.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -N -t -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -N -t -T MD,ia -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  --barcode-tag BC -i --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/i.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  --barcode-tag BC -i --index-format 'i*i*' --i1 /<<PKGBUILDDIR>>/test/i.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -i --index-format 'i*i*' -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.703.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -N -1 /<<PKGBUILDDIR>>/test/o.fq -2 /<<PKGBUILDDIR>>/test/o.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fasta  -N -1 /<<PKGBUILDDIR>>/test/o.fa -2 /<<PKGBUILDDIR>>/test/o.fa /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -N -o /<<PKGBUILDDIR>>/test/o.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -N -s /tmp/kS2G4yOY52/bam2fq.discard.s.fq -0 /tmp/kS2G4yOY52/bam2fq.discard.0.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -T ba,bb,bc,bd,be,bf,bg /<<PKGBUILDDIR>>/test/dat/bam2fq.013.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  --index-format 'i8n1i8' --i1 /<<PKGBUILDDIR>>/test/i1.fq --i2 /<<PKGBUILDDIR>>/test/i2.fq -0 /<<PKGBUILDDIR>>/test/0.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.014.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -N -T '' /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -N -t -T '*' /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -N -T '*' -d MD:10 /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -N -T '*' -d NM:0 /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq  -N -T '*' -d ia /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	Generate BAM file (2 threads)                               .. ok

	Generate CRAM file (2 threads)                              .. ok

	1: fastq  (SAM input) (2 threads)                           [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	2: fastq -n (SAM input) (2 threads)                         [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	3: fastq  (BAM input) (2 threads)                           [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	4: fastq -n (BAM input) (2 threads)                         [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	5: fastq  (CRAM input) (2 threads)                          [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	6: fastq -n (CRAM input) (2 threads)                        [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.002.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.003.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.010.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /<<PKGBUILDDIR>>/test/bc_split.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -t -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -t -T MD,ia -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/i.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /<<PKGBUILDDIR>>/test/i.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -i --index-format 'i*i*' -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.703.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -1 /<<PKGBUILDDIR>>/test/o.fq -2 /<<PKGBUILDDIR>>/test/o.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fasta -@ 2 -N -1 /<<PKGBUILDDIR>>/test/o.fa -2 /<<PKGBUILDDIR>>/test/o.fa /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -o /<<PKGBUILDDIR>>/test/o.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -s /tmp/kS2G4yOY52/bam2fq.discard.s.fq -0 /tmp/kS2G4yOY52/bam2fq.discard.0.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /<<PKGBUILDDIR>>/test/dat/bam2fq.013.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /<<PKGBUILDDIR>>/test/i1.fq --i2 /<<PKGBUILDDIR>>/test/i2.fq -0 /<<PKGBUILDDIR>>/test/0.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.014.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -T '' /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -t -T '*' /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -T '*' -d MD:10 /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -T '*' -d NM:0 /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/<<PKGBUILDDIR>>/samtools fastq -@ 2 -N -T '*' -d ia /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok

test_depad:
	Generate BAM file                                           .. ok

	depad  (SAM input)                                          .. ok

	depad -s (SAM input)                                        .. ok

	depad -u (SAM input)                                        .. ok

	depad -1 (SAM input)                                        .. ok

	depad  (BAM input)                                          .. ok

	depad -s (BAM input)                                        .. ok

	depad -u (BAM input)                                        .. ok

	depad -1 (BAM input)                                        .. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/1_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/1_map_cigar_large.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/4_X_cigar_full_seq.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/5_insert_cigar.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/5_insert_cigar_large.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa -i 0 /<<PKGBUILDDIR>>/test/stat/5_insert_cigar.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/7_supp.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/7_supp_large.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/8_secondary.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/8_secondary_large.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -S RG -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/1_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -S RG -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/10_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -t /<<PKGBUILDDIR>>/test/stat/11.stats.targets /<<PKGBUILDDIR>>/test/stat/11_target.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -g 4 -t /<<PKGBUILDDIR>>/test/stat/11.stats.targets /<<PKGBUILDDIR>>/test/stat/11_target.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -g 4 /<<PKGBUILDDIR>>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/12_overlaps.bam -t /<<PKGBUILDDIR>>/test/stat/12_3reads.bed | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/12_overlaps.bam -p -t /<<PKGBUILDDIR>>/test/stat/12_3reads.bed | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/12_overlaps.bam -t /<<PKGBUILDDIR>>/test/stat/12_2reads.bed | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/12_overlaps.bam -p -t /<<PKGBUILDDIR>>/test/stat/12_2reads.bed | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_ok.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4

	/<<PKGBUILDDIR>>/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4

	/<<PKGBUILDDIR>>/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

test_stats:
	/<<PKGBUILDDIR>>/samtools stats /<<PKGBUILDDIR>>/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4

	/<<PKGBUILDDIR>>/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -I s1 /<<PKGBUILDDIR>>/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -I grp2 /<<PKGBUILDDIR>>/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -I grp3 /<<PKGBUILDDIR>>/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -I Sample /<<PKGBUILDDIR>>/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/mpileup/ce.fa /<<PKGBUILDDIR>>/test/stat/15.big_del.sam | tail -n+4
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.bam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam -b /tmp/uCJsP03Pnd - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -r -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -cp -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a_regex.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b_regex.sam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -o - -s 1 -O sam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/kS2G4yOY52/merge.tag.1.bam /tmp/kS2G4yOY52/merge.tag.2.bam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/kS2G4yOY52/merge.tag.3.bam /tmp/kS2G4yOY52/merge.tag.4.bam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge --no-PG -O SAM - /<<PKGBUILDDIR>>/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge --no-PG -O SAM -L /<<PKGBUILDDIR>>/test/merge/merge.bed - /tmp/kS2G4yOY52/merge.bed.1.bam /tmp/kS2G4yOY52/merge.bed.2.bam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge --no-PG -r -O SAM - /<<PKGBUILDDIR>>/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.bam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam -b /tmp/84J4TgUbDA - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 -r -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 -cp -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -O sam - /<<PKGBUILDDIR>>/test/dat/test_input_1_a_regex.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b_regex.sam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 -o - -s 1 -O sam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/kS2G4yOY52/merge.tag.1.bam /tmp/kS2G4yOY52/merge.tag.2.bam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/kS2G4yOY52/merge.tag.3.bam /tmp/kS2G4yOY52/merge.tag.4.bam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 --no-PG -O SAM - /<<PKGBUILDDIR>>/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 --no-PG -O SAM -L /<<PKGBUILDDIR>>/test/merge/merge.bed - /tmp/kS2G4yOY52/merge.bed.1.bam /tmp/kS2G4yOY52/merge.bed.2.bam
.. ok

test_merge:
	/<<PKGBUILDDIR>>/samtools merge -@ 2 --no-PG -r -O SAM - /<<PKGBUILDDIR>>/test/merge/test_no_pg_rg_co.sam
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/kS2G4yOY52/sortout
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/kS2G4yOY52/sortout.bam
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/kS2G4yOY52/sorttmp
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -n -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -N -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -t RG -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -n -t RG -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -t AS -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -t FI -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort --template-coordinate -m 10M /<<PKGBUILDDIR>>/test/sort/template-coordinate.sort.sam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam | /<<PKGBUILDDIR>>/samtools sort -M -K10 -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam | /<<PKGBUILDDIR>>/samtools sort -M -K10 -I /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam | /<<PKGBUILDDIR>>/samtools sort -MH -K10 -I /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -@ 2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/kS2G4yOY52/sortout
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -@ 2 -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/kS2G4yOY52/sortout.bam
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -@ 2 -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/kS2G4yOY52/sorttmp
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -@ 2 -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -@ 2 -n -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -@ 2 -N -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -@ 2 -t RG -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -@ 2 -n -t RG -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -@ 2 -t AS -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -@ 2 -t FI -m 10M /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools sort -@ 2 --template-coordinate -m 10M /<<PKGBUILDDIR>>/test/sort/template-coordinate.sort.sam -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam | /<<PKGBUILDDIR>>/samtools sort -@ 2 -M -K10 -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam | /<<PKGBUILDDIR>>/samtools sort -@ 2 -M -K10 -I /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_sort:
	/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam | /<<PKGBUILDDIR>>/samtools sort -@ 2 -MH -K10 -I /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_collate:
	/<<PKGBUILDDIR>>/samtools collate --output-fmt=sam -O /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/<<PKGBUILDDIR>>/samtools collate -o /<<PKGBUILDDIR>>/test/collate/collate1.tmp.sam  /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/<<PKGBUILDDIR>>/samtools collate -o /<<PKGBUILDDIR>>/test/collate/collate2.tmp.sam  /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam /<<PKGBUILDDIR>>/test/collate/collate2.tmp
.. ok

test_collate:
	/<<PKGBUILDDIR>>/samtools collate --output-fmt=sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam /<<PKGBUILDDIR>>/test/collate/collate3.tmp
.. ok

test_collate:
	/<<PKGBUILDDIR>>/samtools collate --output-fmt=sam -f /<<PKGBUILDDIR>>/test/collate/fast_collate.sam -o /<<PKGBUILDDIR>>/test/collate/1_fast_collate.sam
.. ok

test_collate:
	/<<PKGBUILDDIR>>/samtools collate --output-fmt=sam -f -r 4 /<<PKGBUILDDIR>>/test/collate/fast_collate.sam -o /<<PKGBUILDDIR>>/test/collate/2_fast_collate_with_tmp.sam
.. ok

test_collate:
	/<<PKGBUILDDIR>>/samtools collate -@ 2 --output-fmt=sam -O /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/<<PKGBUILDDIR>>/samtools collate -@ 2 -o /<<PKGBUILDDIR>>/test/collate/collate1.tmp.sam  /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/<<PKGBUILDDIR>>/samtools collate -@ 2 -o /<<PKGBUILDDIR>>/test/collate/collate2.tmp.sam  /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam /<<PKGBUILDDIR>>/test/collate/collate2.tmp
.. ok

test_collate:
	/<<PKGBUILDDIR>>/samtools collate -@ 2 --output-fmt=sam /<<PKGBUILDDIR>>/test/dat/test_input_1_d.sam /<<PKGBUILDDIR>>/test/collate/collate3.tmp
.. ok

test_collate:
	/<<PKGBUILDDIR>>/samtools collate -@ 2 --output-fmt=sam -f /<<PKGBUILDDIR>>/test/collate/fast_collate.sam -o /<<PKGBUILDDIR>>/test/collate/1_fast_collate.sam
.. ok

test_collate:
	/<<PKGBUILDDIR>>/samtools collate -@ 2 --output-fmt=sam -f -r 4 /<<PKGBUILDDIR>>/test/collate/fast_collate.sam -o /<<PKGBUILDDIR>>/test/collate/2_fast_collate_with_tmp.sam
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/1_coord_sort.sam -

	ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.

.. expected failure

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -z off -O sam /<<PKGBUILDDIR>>/test/fixmate/2_isize_overflow.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -cO sam /<<PKGBUILDDIR>>/test/fixmate/5_ct.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -cO sam /<<PKGBUILDDIR>>/test/fixmate/6_ct_replace.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -z off -O sam /<<PKGBUILDDIR>>/test/fixmate/7_two_read_mapped.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -z off -O sam /<<PKGBUILDDIR>>/test/fixmate/8_isize_overflow_64bit.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/sanitize.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/1_coord_sort.sam -

	ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.

.. expected failure

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -z off -O sam /<<PKGBUILDDIR>>/test/fixmate/2_isize_overflow.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -cO sam /<<PKGBUILDDIR>>/test/fixmate/5_ct.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -cO sam /<<PKGBUILDDIR>>/test/fixmate/6_ct_replace.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -z off -O sam /<<PKGBUILDDIR>>/test/fixmate/7_two_read_mapped.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -z off -O sam /<<PKGBUILDDIR>>/test/fixmate/8_isize_overflow_64bit.sam -
.. ok

test_fixmate:
	/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/sanitize.sam -
.. ok

/<<PKGBUILDDIR>>/samtools calmd -uAr /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa
.. ok

/<<PKGBUILDDIR>>/samtools calmd -@ 2 -uAr /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa
.. ok

test_idxstat:
	/<<PKGBUILDDIR>>/samtools idxstats /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok

test_idxstat:
	/<<PKGBUILDDIR>>/samtools idxstats /<<PKGBUILDDIR>>/test/dat/test_input_1_a.cram
.. ok

test_idxstat:
	/<<PKGBUILDDIR>>/samtools idxstats /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam
.. ok

test_quickcheck:
	/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/1.quickcheck.badeof.bam
.. ok

test_quickcheck:
	/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/2.quickcheck.badheader.bam
.. ok

test_quickcheck:
	/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/3.quickcheck.ok.bam
.. ok

test_quickcheck:
	/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/4.quickcheck.ok.bam
.. ok

test_quickcheck:
	/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/5.quickcheck.scramble30.truncated.cram
.. ok

test_quickcheck:
	/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/6.quickcheck.cram21.ok.cram
.. ok

test_quickcheck:
	/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/7.quickcheck.cram30.ok.cram
.. ok

test_quickcheck:
	/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/8.quickcheck.cram21.truncated.cram
.. ok

test_quickcheck:
	/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/9.quickcheck.cram30.truncated.cram
.. ok

test_quickcheck:
	/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/10.quickcheck.notargets.bam
.. ok

test_quickcheck:
	/<<PKGBUILDDIR>>/samtools quickcheck -v  /<<PKGBUILDDIR>>/test/quickcheck/1.quickcheck.badeof.bam /<<PKGBUILDDIR>>/test/quickcheck/2.quickcheck.badheader.bam /<<PKGBUILDDIR>>/test/quickcheck/3.quickcheck.ok.bam /<<PKGBUILDDIR>>/test/quickcheck/4.quickcheck.ok.bam /<<PKGBUILDDIR>>/test/quickcheck/5.quickcheck.scramble30.truncated.cram /<<PKGBUILDDIR>>/test/quickcheck/6.quickcheck.cram21.ok.cram /<<PKGBUILDDIR>>/test/quickcheck/7.quickcheck.cram30.ok.cram /<<PKGBUILDDIR>>/test/quickcheck/8.quickcheck.cram21.truncated.cram /<<PKGBUILDDIR>>/test/quickcheck/9.quickcheck.cram30.truncated.cram /<<PKGBUILDDIR>>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok

test_quickcheck:
	/<<PKGBUILDDIR>>/samtools quickcheck -uv /<<PKGBUILDDIR>>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok

test_reheader:
	/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.bam | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/<<PKGBUILDDIR>>/samtools reheader --in-place /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram && /<<PKGBUILDDIR>>/samtools view -h --no-PG /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/<<PKGBUILDDIR>>/samtools reheader --in-place /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram && /<<PKGBUILDDIR>>/samtools view -h --no-PG /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/<<PKGBUILDDIR>>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<<PKGBUILDDIR>>/test/dat/view.001.tmp.bam | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/<<PKGBUILDDIR>>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | /<<PKGBUILDDIR>>/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m overwrite_all /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m orphan_only /<<PKGBUILDDIR>>/test/addrprg/2_fixup_orphan.sam
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -R '1#9' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -m overwrite_all /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -m orphan_only /<<PKGBUILDDIR>>/test/addrprg/2_fixup_orphan.sam
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -R '1#9' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/1_name_sort.sam -

	ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate.


.. expected failure

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/2_bad_order.sam -

	ERR: samtools markdup: error, not in coordinate sorted order.


.. expected failure

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/3_missing_mc.sam -

	ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first.

samtools markdup: error, unable to assign pair hash key.


.. expected failure

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/4_missing_ms.sam -

	ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.

samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.


.. expected failure

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/5_markdup.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -O sam -r --no-PG /<<PKGBUILDDIR>>/test/markdup/6_remove_dups.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -S -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/7_mark_supp_dup.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/8_optical_dup.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /<<PKGBUILDDIR>>/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /<<PKGBUILDDIR>>/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /<<PKGBUILDDIR>>/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /<<PKGBUILDDIR>>/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /<<PKGBUILDDIR>>/test/markdup/12_optical_chain_regex.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/13_optical_barcode_tag.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/14_optical_barcode_name.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/15_optical_barcode_rgx_name.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/17_read_group.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /<<PKGBUILDDIR>>/test/markdup/18_primary_duplicate_count.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/1_name_sort.sam -

	ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate.


.. expected failure

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/2_bad_order.sam -

	ERR: samtools markdup: error, not in coordinate sorted order.


.. expected failure

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/3_missing_mc.sam -

	ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first.

samtools markdup: error, unable to assign pair hash key.


.. expected failure

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/4_missing_ms.sam -

	ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.

samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.


.. expected failure

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/5_markdup.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -O sam -r --no-PG /<<PKGBUILDDIR>>/test/markdup/6_remove_dups.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/7_mark_supp_dup.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/8_optical_dup.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /<<PKGBUILDDIR>>/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /<<PKGBUILDDIR>>/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /<<PKGBUILDDIR>>/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /<<PKGBUILDDIR>>/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /<<PKGBUILDDIR>>/test/markdup/12_optical_chain_regex.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/13_optical_barcode_tag.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/14_optical_barcode_name.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/15_optical_barcode_rgx_name.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/17_read_group.sam -
.. ok

test_markdup:
	/<<PKGBUILDDIR>>/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /<<PKGBUILDDIR>>/test/markdup/18_primary_duplicate_count.sam -
.. ok

test_bedcov:
	/<<PKGBUILDDIR>>/samtools bedcov /<<PKGBUILDDIR>>/test/bedcov/bedcov.bed /<<PKGBUILDDIR>>/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/<<PKGBUILDDIR>>/samtools bedcov -j /<<PKGBUILDDIR>>/test/bedcov/bedcov.bed /<<PKGBUILDDIR>>/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/<<PKGBUILDDIR>>/samtools bedcov -g512 -G2048 /<<PKGBUILDDIR>>/test/bedcov/bedcov_gG.bed /<<PKGBUILDDIR>>/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/<<PKGBUILDDIR>>/samtools bedcov -c /<<PKGBUILDDIR>>/test/bedcov/bedcov_gG.bed /<<PKGBUILDDIR>>/test/bedcov/bedcov.bam
.. ok

test_split:
	/<<PKGBUILDDIR>>/samtools split  --output-fmt sam -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok

test_split:
	/<<PKGBUILDDIR>>/samtools split  --output-fmt sam -d RG -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok

test_split:
	/<<PKGBUILDDIR>>/samtools split  --output-fmt sam -d an -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok

test_split:
	/<<PKGBUILDDIR>>/samtools split  --output-fmt sam -d an -M 3 -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok

test_split:
	/<<PKGBUILDDIR>>/samtools split  -@ 2 --output-fmt sam -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok

test_split:
	/<<PKGBUILDDIR>>/samtools split  -@ 2 --output-fmt sam -d RG -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok

test_split:
	/<<PKGBUILDDIR>>/samtools split  -@ 2 --output-fmt sam -d an -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok

test_split:
	/<<PKGBUILDDIR>>/samtools split  -@ 2 --output-fmt sam -d an -M 3 -u /<<PKGBUILDDIR>>/test/split/split.tmp.unk.sam -f /<<PKGBUILDDIR>>/test/split/split.tmp.%!.%. /<<PKGBUILDDIR>>/test/split/split.sam
.. ok

test_large_positions:
	/<<PKGBUILDDIR>>/samtools view -h --no-PG /tmp/kS2G4yOY52/longref.sam.gz
.. ok

test_large_positions:
	/<<PKGBUILDDIR>>/samtools view -h --no-PG /tmp/kS2G4yOY52/longref.sam.gz CHROMOSOME_I:10000000114-10000000168
.. ok

test_large_positions:
	/<<PKGBUILDDIR>>/samtools view -h --no-PG -L /<<PKGBUILDDIR>>/test/large_pos/test.bed /tmp/kS2G4yOY52/longref.sam.gz
.. ok

test_large_positions:
	/<<PKGBUILDDIR>>/samtools sort -O sam --no-PG -m 10M /<<PKGBUILDDIR>>/test/large_pos/longref_name.sam
.. ok

test_large_positions:
	/<<PKGBUILDDIR>>/samtools merge -O sam --no-PG - /<<PKGBUILDDIR>>/test/large_pos/longref.sam /<<PKGBUILDDIR>>/test/large_pos/longref2.sam
.. ok

test_large_positions:
	/<<PKGBUILDDIR>>/samtools depth /<<PKGBUILDDIR>>/test/large_pos/longref.sam
.. ok

test_large_positions:
	/<<PKGBUILDDIR>>/samtools depth -b /<<PKGBUILDDIR>>/test/large_pos/test.bed /<<PKGBUILDDIR>>/test/large_pos/longref.sam
.. ok

test_large_positions:
	/<<PKGBUILDDIR>>/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/kS2G4yOY52/longref.sam.gz
.. ok

test_large_positions:
	/<<PKGBUILDDIR>>/samtools sort    -O sam --no-PG -n -m 10M test/large_pos/longref3.sam |
                     /<<PKGBUILDDIR>>/samtools fixmate -O sam --no-PG - - |
                     /<<PKGBUILDDIR>>/samtools sort    -O sam --no-PG -m 10M
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG  --keep-tag --output-fmt=sam --original -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --output-fmt=sam -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG  --keep-tag --output-fmt=sam --strand --both-ends -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/2_both_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test2.bed /<<PKGBUILDDIR>>/test/ampliconclip/4_total_hc_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG  --keep-tag --output-fmt=sam --original -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG  --keep-tag --output-fmt=sam --strand --both-ends -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/2_both_test_data.sam
.. ok

test_ampliconclip:
	/<<PKGBUILDDIR>>/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /<<PKGBUILDDIR>>/test/ampliconclip/ac_test2.bed /<<PKGBUILDDIR>>/test/ampliconclip/4_total_hc_data.sam
.. ok

test_ampliconstats:
	/<<PKGBUILDDIR>>/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconclip/1_hard_clipped.expected.sam /<<PKGBUILDDIR>>/test/ampliconclip/1_soft_clipped.expected.sam /<<PKGBUILDDIR>>/test/ampliconclip/1_soft_clipped_strand.expected.sam /<<PKGBUILDDIR>>/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line'
.. ok

test_ampliconstats:
	/<<PKGBUILDDIR>>/samtools ampliconstats -@ 2 -c 0 /<<PKGBUILDDIR>>/test/ampliconclip/multi_ref.bed /<<PKGBUILDDIR>>/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line'
.. ok

test_ampliconstats:
	/<<PKGBUILDDIR>>/samtools ampliconstats -@ 2 -c 0 /<<PKGBUILDDIR>>/test/ampliconclip/ac_test.bed /<<PKGBUILDDIR>>/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line'
.. ok

test_reset:
	cat /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam | /<<PKGBUILDDIR>>/samtools reset | /<<PKGBUILDDIR>>/samtools view
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset < /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam | /<<PKGBUILDDIR>>/samtools view
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam | /<<PKGBUILDDIR>>/samtools view
.. ok

test_reset:
	cat /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam | /<<PKGBUILDDIR>>/samtools reset -o /<<PKGBUILDDIR>>/test/reset/output.tmp.sam
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset -o /<<PKGBUILDDIR>>/test/reset/output.tmp.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset -o /<<PKGBUILDDIR>>/test/reset/output.tmp.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_a.cram
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa_index /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam -o /<<PKGBUILDDIR>>/test/reset/output.tmp.sam; grep /<<PKGBUILDDIR>>/test/reset/output.tmp.sam -e"@PG	ID:samtools	PN:samtools" | wc -l | sed 's/ //g'
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset --reject-PG sam_to_fixed_bam /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam -o /<<PKGBUILDDIR>>/test/reset/output.tmp.sam; grep /<<PKGBUILDDIR>>/test/reset/output.tmp.sam -e"@PG	ID:" | wc -l | sed 's/ //g'
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa_index --no-PG /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam -o /<<PKGBUILDDIR>>/test/reset/output.tmp.sam; grep /<<PKGBUILDDIR>>/test/reset/output.tmp.sam -e"@PG"
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG -o /<<PKGBUILDDIR>>/test/reset/output
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /<<PKGBUILDDIR>>/test/reset/output
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /<<PKGBUILDDIR>>/test/reset/output
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /<<PKGBUILDDIR>>/test/reset/output
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /<<PKGBUILDDIR>>/test/reset/output
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /<<PKGBUILDDIR>>/test/reset/output
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset --reject-PG bwa /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /<<PKGBUILDDIR>>/test/reset/output
.. ok

test_reset:
	/<<PKGBUILDDIR>>/samtools reset /<<PKGBUILDDIR>>/test/reset/seq.sam -o /<<PKGBUILDDIR>>/test/reset/output
.. ok


Number of tests:
    total            .. 933
    passed           .. 889
    failed           .. 0
    expected failure .. 44
    unexpected pass  .. 0

test/merge/test_bam_translate test/merge/test_bam_translate.tmp
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
cd test/mpileup && AWK="mawk" ../regression.sh mpileup.reg

=== Testing mpileup.reg regressions ===
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"

EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam

Expected   passes:   118
Unexpected passes:   0
Expected   failures: 1
Unexpected failures: 0
=> PASS
cd test/mpileup && AWK="mawk" ../regression.sh depth.reg

=== Testing depth.reg regressions ===

EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools depth -a -b xx.bed3 xx#depth3.bam

Expected   passes:   53
Unexpected passes:   0
Expected   failures: 1
Unexpected failures: 0
=> PASS
cd test/consensus && AWK="mawk" ../regression.sh consensus.reg

=== Testing consensus.reg regressions ===

Expected   passes:   65
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
cd test/cram_size && AWK="mawk" ../regression.sh cram_size.reg

=== Testing cram_size.reg regressions ===

Expected   passes:   3
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
	rm -fr -- /tmp/dh-xdg-rundir-oetl5BbW
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
   dh_prep -a
	rm -f -- debian/samtools.substvars
	rm -fr -- debian/.debhelper/generated/samtools/ debian/samtools/ debian/tmp/
	rm -f debian/samtools.debhelper.log
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install -- \
  prefix=/usr
	install -m0755 -d /<<PKGBUILDDIR>>/debian/tmp
	make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
make[2]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp/usr/bin /<<PKGBUILDDIR>>/debian/tmp/usr/bin /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
install -p samtools /<<PKGBUILDDIR>>/debian/tmp/usr/bin
install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /<<PKGBUILDDIR>>/debian/tmp/usr/bin
install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /<<PKGBUILDDIR>>/debian/tmp/usr/bin
install -p -m 644 doc/samtools*.1 misc/wgsim.1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam*
cd test/reference && rm -f mpileup.*.fai
rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o
rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
	rm -f debian/samtools.debhelper.log
   debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
	install -m0755 -d debian/samtools//usr
	cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
	install -m0755 -d debian/samtools//usr/share/man
	cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
	install -m0755 -d debian/samtools/usr/share/commonwl/
	cp --reflink=auto -a ./debian/samtools-faidx.cwl ./debian/samtools-index.cwl ./debian/samtools-rmdup.cwl ./debian/samtools-sort.cwl ./debian/samtools-view.cwl debian/samtools/usr/share/commonwl//
	install -m0755 -d debian/samtools/usr/share/man/man1
	cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
# Fix Perl interpreter PATH
for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \
    sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \
done
# Disable the executable bit on a dataset.
if [ -d debian/samtools-test ] \
; then chmod 0644 debian/samtools-test/usr/share/samtools/test/ampliconclip/ac_test.bed \
; fi
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installdocs -a
	install -m0755 -d debian/samtools/usr/share/doc/samtools
	install -m0755 -d debian/samtools/usr/share/doc/samtools
	cp --reflink=auto -a ./AUTHORS debian/samtools/usr/share/doc/samtools
	cp --reflink=auto -a ./README debian/samtools/usr/share/doc/samtools
	cp --reflink=auto -a ./debian/README.test debian/samtools/usr/share/doc/samtools
	chmod -R u\+rw,go=rX debian/samtools/usr/share/doc
	install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
	install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
	rm -f debian/samtools.debhelper.log
   debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs NEWS.md
	install -m0755 -d debian/samtools/usr/share/doc/samtools
	install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed debian/samtools/usr/share/doc/samtools/changelog.Debian
	install -p -m0644 NEWS.md debian/samtools/usr/share/doc/samtools/changelog
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installexamples -a
	install -m0755 -d debian/samtools/usr/share/doc/samtools/examples
	cp --reflink=auto -a ./examples/00README.txt debian/samtools/usr/share/doc/samtools/examples
	cp --reflink=auto -a ./examples/ex1.fa debian/samtools/usr/share/doc/samtools/examples
	cp --reflink=auto -a ./examples/ex1.sam.gz debian/samtools/usr/share/doc/samtools/examples
	cp --reflink=auto -a ./examples/toy.fa debian/samtools/usr/share/doc/samtools/examples
	cp --reflink=auto -a ./examples/toy.sam debian/samtools/usr/share/doc/samtools/examples
	rm -f debian/samtools.debhelper.log
   debian/rules execute_before_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# Fix whatis entries for subcommands; "samtools subcommand \- desc."
# will confuse the lexer, but "samtools-subcommand \- desc." will work.
sed -i '/^\.SH NAME/{n;s/^\([^ ]\+\) \([^ ]\+\) \\- /\1-\2 \\- /}' \
	debian/*/usr/share/man/man*/*.*
# .EX expects a indentation width.
sed -i 's/^.EX$/.EX 8/' debian/*/usr/share/man/man*/*.*
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installman -a
	rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1
	ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1
	mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1
	mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1
	mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1
	mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1
	mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1
	mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1
	mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1
	mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1
	mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1
	mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1
	mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1
	chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1
	mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1
	mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1
	mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1
	mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1
	mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1
	mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1
	mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1
	mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1
	mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1
	mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1
	mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1
	chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1
	mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1
	mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1
	mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1
	mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1
	mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1
	mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1
	mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1
	mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1
	mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1
	mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1
	chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1
	mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1
	mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1
	mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1
	mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1
	mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1
	mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1
	mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1
	mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1
	mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1
	mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1
	mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1
	chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1
   dh_lintian -a
	install -m0755 -d debian/samtools/usr/share/lintian/overrides
	install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
   dh_perl -a
	mv debian/samtools.substvars.new debian/samtools.substvars
   dh_link -a
	rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1
	ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1
   dh_strip_nondeterminism -a
	Using 1708190561 as canonical time
	Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip
   dh_compress -a
	cd debian/samtools
	chmod a-x usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
	gzip -9nf usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
	cd '/<<PKGBUILDDIR>>'
	rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz
	ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz
   dh_fixperms -a
	find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/samtools -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/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
   dh_missing -a
   dh_dwz -a
	install -m0755 -d debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf
	dwz -mdebian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim
dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 694306 new size 715703
	objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug
	chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug
   dh_strip -a
	debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/ace2sam
debugedit: debian/samtools/usr/bin/ace2sam: Unknown DWARF DW_FORM_0x1f21
41000176e4688d53f842090ec71ff6c4568345ee
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/41
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/41/000176e4688d53f842090ec71ff6c4568345ee.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/41/000176e4688d53f842090ec71ff6c4568345ee.debug
	strip --remove-section=.comment --remove-section=.note -o /tmp/i1RxsqSWwf/stripNQ3f3d debian/samtools/usr/bin/ace2sam
	chmod --reference debian/samtools/usr/bin/ace2sam /tmp/i1RxsqSWwf/stripNQ3f3d
	cat '/tmp/i1RxsqSWwf/stripNQ3f3d' > 'debian/samtools/usr/bin/ace2sam'
	chmod --reference /tmp/i1RxsqSWwf/stripNQ3f3d debian/samtools/usr/bin/ace2sam
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/41/000176e4688d53f842090ec71ff6c4568345ee.debug debian/samtools/usr/bin/ace2sam /tmp/i1RxsqSWwf/objcopyU8z5q3
	chmod --reference debian/samtools/usr/bin/ace2sam /tmp/i1RxsqSWwf/objcopyU8z5q3
	cat '/tmp/i1RxsqSWwf/objcopyU8z5q3' > 'debian/samtools/usr/bin/ace2sam'
	chmod --reference /tmp/i1RxsqSWwf/objcopyU8z5q3 debian/samtools/usr/bin/ace2sam
	debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/maq2sam-long
debugedit: debian/samtools/usr/bin/maq2sam-long: Unknown DWARF DW_FORM_0x1f20
e7f4ede9a6bd7712f10b0c944969bba7ca61ea4e
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7/f4ede9a6bd7712f10b0c944969bba7ca61ea4e.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7/f4ede9a6bd7712f10b0c944969bba7ca61ea4e.debug
	strip --remove-section=.comment --remove-section=.note -o /tmp/i1RxsqSWwf/stripKkhJCn debian/samtools/usr/bin/maq2sam-long
	chmod --reference debian/samtools/usr/bin/maq2sam-long /tmp/i1RxsqSWwf/stripKkhJCn
	cat '/tmp/i1RxsqSWwf/stripKkhJCn' > 'debian/samtools/usr/bin/maq2sam-long'
	chmod --reference /tmp/i1RxsqSWwf/stripKkhJCn debian/samtools/usr/bin/maq2sam-long
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7/f4ede9a6bd7712f10b0c944969bba7ca61ea4e.debug debian/samtools/usr/bin/maq2sam-long /tmp/i1RxsqSWwf/objcopygmhJC8
	chmod --reference debian/samtools/usr/bin/maq2sam-long /tmp/i1RxsqSWwf/objcopygmhJC8
	cat '/tmp/i1RxsqSWwf/objcopygmhJC8' > 'debian/samtools/usr/bin/maq2sam-long'
	chmod --reference /tmp/i1RxsqSWwf/objcopygmhJC8 debian/samtools/usr/bin/maq2sam-long
	debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/md5fa
debugedit: debian/samtools/usr/bin/md5fa: Unknown DWARF DW_FORM_0x1f21
c6d615d632ee904b2a2952b6a4165adb143a4c34
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/d615d632ee904b2a2952b6a4165adb143a4c34.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/d615d632ee904b2a2952b6a4165adb143a4c34.debug
	strip --remove-section=.comment --remove-section=.note -o /tmp/i1RxsqSWwf/stripjQ22mi debian/samtools/usr/bin/md5fa
	chmod --reference debian/samtools/usr/bin/md5fa /tmp/i1RxsqSWwf/stripjQ22mi
	cat '/tmp/i1RxsqSWwf/stripjQ22mi' > 'debian/samtools/usr/bin/md5fa'
	chmod --reference /tmp/i1RxsqSWwf/stripjQ22mi debian/samtools/usr/bin/md5fa
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/d615d632ee904b2a2952b6a4165adb143a4c34.debug debian/samtools/usr/bin/md5fa /tmp/i1RxsqSWwf/objcopyO5VlOa
	chmod --reference debian/samtools/usr/bin/md5fa /tmp/i1RxsqSWwf/objcopyO5VlOa
	cat '/tmp/i1RxsqSWwf/objcopyO5VlOa' > 'debian/samtools/usr/bin/md5fa'
	chmod --reference /tmp/i1RxsqSWwf/objcopyO5VlOa debian/samtools/usr/bin/md5fa
	debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/wgsim
debugedit: debian/samtools/usr/bin/wgsim: Unknown DWARF DW_FORM_0x1f20
2b8a9aa90a9d154aef362e21c6450e5f8ce81c96
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2b
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2b/8a9aa90a9d154aef362e21c6450e5f8ce81c96.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2b/8a9aa90a9d154aef362e21c6450e5f8ce81c96.debug
	strip --remove-section=.comment --remove-section=.note -o /tmp/i1RxsqSWwf/stripZSkmZE debian/samtools/usr/bin/wgsim
	chmod --reference debian/samtools/usr/bin/wgsim /tmp/i1RxsqSWwf/stripZSkmZE
	cat '/tmp/i1RxsqSWwf/stripZSkmZE' > 'debian/samtools/usr/bin/wgsim'
	chmod --reference /tmp/i1RxsqSWwf/stripZSkmZE debian/samtools/usr/bin/wgsim
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2b/8a9aa90a9d154aef362e21c6450e5f8ce81c96.debug debian/samtools/usr/bin/wgsim /tmp/i1RxsqSWwf/objcopyNUVr57
	chmod --reference debian/samtools/usr/bin/wgsim /tmp/i1RxsqSWwf/objcopyNUVr57
	cat '/tmp/i1RxsqSWwf/objcopyNUVr57' > 'debian/samtools/usr/bin/wgsim'
	chmod --reference /tmp/i1RxsqSWwf/objcopyNUVr57 debian/samtools/usr/bin/wgsim
	debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/maq2sam-short
debugedit: debian/samtools/usr/bin/maq2sam-short: Unknown DWARF DW_FORM_0x1f20
cd3a00b7bb0203419d897b8edee35d9f09517021
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/3a00b7bb0203419d897b8edee35d9f09517021.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/3a00b7bb0203419d897b8edee35d9f09517021.debug
	strip --remove-section=.comment --remove-section=.note -o /tmp/i1RxsqSWwf/stripDZe7iF debian/samtools/usr/bin/maq2sam-short
	chmod --reference debian/samtools/usr/bin/maq2sam-short /tmp/i1RxsqSWwf/stripDZe7iF
	cat '/tmp/i1RxsqSWwf/stripDZe7iF' > 'debian/samtools/usr/bin/maq2sam-short'
	chmod --reference /tmp/i1RxsqSWwf/stripDZe7iF debian/samtools/usr/bin/maq2sam-short
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/3a00b7bb0203419d897b8edee35d9f09517021.debug debian/samtools/usr/bin/maq2sam-short /tmp/i1RxsqSWwf/objcopyq5nzaK
	chmod --reference debian/samtools/usr/bin/maq2sam-short /tmp/i1RxsqSWwf/objcopyq5nzaK
	cat '/tmp/i1RxsqSWwf/objcopyq5nzaK' > 'debian/samtools/usr/bin/maq2sam-short'
	chmod --reference /tmp/i1RxsqSWwf/objcopyq5nzaK debian/samtools/usr/bin/maq2sam-short
	debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/md5sum-lite
debugedit: debian/samtools/usr/bin/md5sum-lite: Unknown DWARF DW_FORM_0x1f20
c699397ceb34bd3c9b14ab8274293c2322a205a9
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/99397ceb34bd3c9b14ab8274293c2322a205a9.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/99397ceb34bd3c9b14ab8274293c2322a205a9.debug
	strip --remove-section=.comment --remove-section=.note -o /tmp/i1RxsqSWwf/strip4azrvh debian/samtools/usr/bin/md5sum-lite
	chmod --reference debian/samtools/usr/bin/md5sum-lite /tmp/i1RxsqSWwf/strip4azrvh
	cat '/tmp/i1RxsqSWwf/strip4azrvh' > 'debian/samtools/usr/bin/md5sum-lite'
	chmod --reference /tmp/i1RxsqSWwf/strip4azrvh debian/samtools/usr/bin/md5sum-lite
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/99397ceb34bd3c9b14ab8274293c2322a205a9.debug debian/samtools/usr/bin/md5sum-lite /tmp/i1RxsqSWwf/objcopyd_7Jm3
	chmod --reference debian/samtools/usr/bin/md5sum-lite /tmp/i1RxsqSWwf/objcopyd_7Jm3
	cat '/tmp/i1RxsqSWwf/objcopyd_7Jm3' > 'debian/samtools/usr/bin/md5sum-lite'
	chmod --reference /tmp/i1RxsqSWwf/objcopyd_7Jm3 debian/samtools/usr/bin/md5sum-lite
	debugedit --build-id --build-id-seed=samtools/1.19.2-1 debian/samtools/usr/bin/samtools
691c8a0d521adfdc4aabbd2a448bb8f9723dd121
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/69
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/69/1c8a0d521adfdc4aabbd2a448bb8f9723dd121.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/69/1c8a0d521adfdc4aabbd2a448bb8f9723dd121.debug
	strip --remove-section=.comment --remove-section=.note -o /tmp/i1RxsqSWwf/strippekLT7 debian/samtools/usr/bin/samtools
	chmod --reference debian/samtools/usr/bin/samtools /tmp/i1RxsqSWwf/strippekLT7
	cat '/tmp/i1RxsqSWwf/strippekLT7' > 'debian/samtools/usr/bin/samtools'
	chmod --reference /tmp/i1RxsqSWwf/strippekLT7 debian/samtools/usr/bin/samtools
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/69/1c8a0d521adfdc4aabbd2a448bb8f9723dd121.debug debian/samtools/usr/bin/samtools /tmp/i1RxsqSWwf/objcopyBq9Evd
	chmod --reference debian/samtools/usr/bin/samtools /tmp/i1RxsqSWwf/objcopyBq9Evd
	cat '/tmp/i1RxsqSWwf/objcopyBq9Evd' > 'debian/samtools/usr/bin/samtools'
	chmod --reference /tmp/i1RxsqSWwf/objcopyBq9Evd debian/samtools/usr/bin/samtools
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz
	cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz
	rm -fr debian/samtools/usr/lib/debug/.dwz
	rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
	ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym
	install -m0755 -d debian/.debhelper/samtools
   dh_makeshlibs -a
	rm -f debian/samtools/DEBIAN/shlibs
   dh_shlibdeps -a
	install -m0755 -d debian/samtools/DEBIAN
	dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools
   dh_installdeb -a
	install -m0755 -d debian/samtools/DEBIAN
   dh_gencontrol -a
	install -m0755 -d debian/samtools/DEBIAN
	echo misc:Depends= >> debian/samtools.substvars
	echo misc:Pre-Depends= >> debian/samtools.substvars
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
	dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=2b8a9aa90a9d154aef362e21c6450e5f8ce81c96 41000176e4688d53f842090ec71ff6c4568345ee 691c8a0d521adfdc4aabbd2a448bb8f9723dd121 c699397ceb34bd3c9b14ab8274293c2322a205a9 c6d615d632ee904b2a2952b6a4165adb143a4c34 cd3a00b7bb0203419d897b8edee35d9f09517021 e7f4ede9a6bd7712f10b0c944969bba7ca61ea4e" -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks
dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
	dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined
	chmod 0644 -- debian/samtools/DEBIAN/control
   dh_md5sums -a
	install -m0755 -d debian/samtools/DEBIAN
	cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/samtools/DEBIAN/md5sums
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
	cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
   dh_builddeb -a
	dpkg-deb --root-owner-group --build debian/samtools ..
	dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root debian/.debhelper/scratch-space/build-samtools
INFO: pkgstriptranslations version 154
INFO: pkgstriptranslations version 154
pkgstriptranslations: processing samtools (in debian/samtools); do_strip: , oemstrip: 
pkgstriptranslations: processing samtools-dbgsym (in debian/.debhelper/samtools/dbgsym-root); do_strip: , oemstrip: 
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgstripfiles: processing control file: debian/samtools/DEBIAN/control, package samtools, directory debian/samtools
.. removing usr/share/doc/samtools/changelog.gz
pkgstripfiles: processing control file: debian/.debhelper/samtools/dbgsym-root/DEBIAN/control, package samtools-dbgsym, directory debian/.debhelper/samtools/dbgsym-root
pkgstripfiles: Running PNG optimization (using 4 cpus) for package samtools ...
dpkg-deb: building package 'samtools-dbgsym' in 'debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.19.2-1_armhf.deb'.
pkgstripfiles: No PNG files.
dpkg-deb: building package 'samtools' in '../samtools_1.19.2-1_armhf.deb'.
	Renaming samtools-dbgsym_1.19.2-1_armhf.deb to samtools-dbgsym_1.19.2-1_armhf.ddeb
	mv debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.19.2-1_armhf.deb ../samtools-dbgsym_1.19.2-1_armhf.ddeb
 dpkg-genbuildinfo --build=any -O../samtools_1.19.2-1_armhf.buildinfo
 dpkg-genchanges --build=any -mLaunchpad Build Daemon <buildd@bos03-arm64-022.buildd> -O../samtools_1.19.2-1_armhf.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 samtools-1.19.2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2024-02-18T05:20:05Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


samtools_1.19.2-1_armhf.changes:
--------------------------------

Format: 1.8
Date: Sat, 17 Feb 2024 18:22:41 +0100
Source: samtools
Binary: samtools
Built-For-Profiles: noudeb
Architecture: armhf
Version: 1.19.2-1
Distribution: noble-proposed
Urgency: medium
Maintainer: Launchpad Build Daemon <buildd@bos03-arm64-022.buildd>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
 samtools   - processing sequence alignments in SAM, BAM and CRAM formats
Changes:
 samtools (1.19.2-1) unstable; urgency=medium
 .
   * [3f34445] New upstream version 1.19.2
   * [e0d4f37] d/control: replace pkg-config by pkgconf.
Checksums-Sha1:
 14ce8e4ff331a63eae7ab1fb8ce3271e5ac96d96 945670 samtools-dbgsym_1.19.2-1_armhf.ddeb
 54c9259efbbeb8583f2c863aab4e82ed2eb408d3 6910 samtools_1.19.2-1_armhf.buildinfo
 396473403f211032b7600ef7a87b658128da9392 601904 samtools_1.19.2-1_armhf.deb
Checksums-Sha256:
 2bb96297d07372a92846b6701ac65ad967a353164be741a8775857e5f4979ed4 945670 samtools-dbgsym_1.19.2-1_armhf.ddeb
 007e03b6cc9271663b2738f694994c1b9af847dc9eee37ad5b7b92df56eb5158 6910 samtools_1.19.2-1_armhf.buildinfo
 51227cdfbe07a0f1af60b7fd92d7bdb12b41224a2be0f2046d7ee5b4ae60144c 601904 samtools_1.19.2-1_armhf.deb
Files:
 29636a1f46ad84f74c9da52f6715d8d4 945670 debug optional samtools-dbgsym_1.19.2-1_armhf.ddeb
 d7a82c1a4bdf303fec07d5cb46c21dd7 6910 science optional samtools_1.19.2-1_armhf.buildinfo
 174dab5723e7e39d465b041d7219fc32 601904 science optional samtools_1.19.2-1_armhf.deb
/<<BUILDDIR>>/samtools_1.19.2-1_armhf.changes.new could not be renamed to /<<BUILDDIR>>/samtools_1.19.2-1_armhf.changes: Illegal seek
Distribution field may be wrong!!!
+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: samtools
Binary: samtools samtools-dbgsym
Architecture: armhf
Version: 1.19.2-1
Checksums-Md5:
 29636a1f46ad84f74c9da52f6715d8d4 945670 samtools-dbgsym_1.19.2-1_armhf.ddeb
 174dab5723e7e39d465b041d7219fc32 601904 samtools_1.19.2-1_armhf.deb
Checksums-Sha1:
 14ce8e4ff331a63eae7ab1fb8ce3271e5ac96d96 945670 samtools-dbgsym_1.19.2-1_armhf.ddeb
 396473403f211032b7600ef7a87b658128da9392 601904 samtools_1.19.2-1_armhf.deb
Checksums-Sha256:
 2bb96297d07372a92846b6701ac65ad967a353164be741a8775857e5f4979ed4 945670 samtools-dbgsym_1.19.2-1_armhf.ddeb
 51227cdfbe07a0f1af60b7fd92d7bdb12b41224a2be0f2046d7ee5b4ae60144c 601904 samtools_1.19.2-1_armhf.deb
Build-Origin: Ubuntu
Build-Architecture: armhf
Build-Date: Sun, 18 Feb 2024 05:20:05 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
 merged-usr-via-aliased-dirs
 usr-local-has-programs
Installed-Build-Depends:
 autoconf (= 2.71-3),
 autoconf-archive (= 20220903-3),
 automake (= 1:1.16.5-1.3ubuntu1),
 autopoint (= 0.21-14ubuntu1),
 autotools-dev (= 20220109.1),
 base-files (= 13ubuntu6),
 base-passwd (= 3.6.3),
 bash (= 5.2.21-2ubuntu1),
 bash-completion (= 1:2.11-8),
 binutils (= 2.42-2ubuntu1),
 binutils-arm-linux-gnueabihf (= 2.42-2ubuntu1),
 binutils-common (= 2.42-2ubuntu1),
 bsdextrautils (= 2.39.2-6ubuntu1),
 bsdutils (= 1:2.39.2-6ubuntu1),
 build-essential (= 12.10ubuntu1),
 bzip2 (= 1.0.8-5build1),
 coreutils (= 9.4-2ubuntu3),
 cpp (= 4:13.2.0-7ubuntu1),
 cpp-13 (= 13.2.0-13ubuntu1),
 cpp-13-arm-linux-gnueabihf (= 13.2.0-13ubuntu1),
 cpp-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu1),
 dash (= 0.5.12-6ubuntu1),
 debconf (= 1.5.86),
 debhelper (= 13.13ubuntu1),
 debianutils (= 5.16),
 debugedit (= 1:5.0-5),
 dh-autoreconf (= 20),
 dh-strip-nondeterminism (= 1.13.1-1),
 diffutils (= 1:3.10-1),
 dpkg (= 1.22.4ubuntu3),
 dpkg-dev (= 1.22.4ubuntu3),
 dwz (= 0.15-1),
 file (= 1:5.45-2),
 findutils (= 4.9.0-5),
 g++ (= 4:13.2.0-7ubuntu1),
 g++-13 (= 13.2.0-13ubuntu1),
 g++-13-arm-linux-gnueabihf (= 13.2.0-13ubuntu1),
 g++-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu1),
 gcc (= 4:13.2.0-7ubuntu1),
 gcc-13 (= 13.2.0-13ubuntu1),
 gcc-13-arm-linux-gnueabihf (= 13.2.0-13ubuntu1),
 gcc-13-base (= 13.2.0-13ubuntu1),
 gcc-14-base (= 14-20240201-3ubuntu1),
 gcc-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu1),
 gettext (= 0.21-14ubuntu1),
 gettext-base (= 0.21-14ubuntu1),
 grep (= 3.11-4),
 groff-base (= 1.23.0-3),
 gzip (= 1.12-1ubuntu1),
 hostname (= 3.23+nmu1ubuntu1),
 init-system-helpers (= 1.66ubuntu1),
 intltool-debian (= 0.35.0+20060710.6),
 libacl1 (= 2.3.1-4ubuntu1),
 libarchive-zip-perl (= 1.68-1),
 libasan8 (= 14-20240201-3ubuntu1),
 libatomic1 (= 14-20240201-3ubuntu1),
 libattr1 (= 1:2.5.2-1),
 libaudit-common (= 1:3.1.2-2),
 libaudit1 (= 1:3.1.2-2),
 libbinutils (= 2.42-2ubuntu1),
 libblkid1 (= 2.39.2-6ubuntu1),
 libbrotli1 (= 1.1.0-2),
 libbz2-1.0 (= 1.0.8-5build1),
 libbz2-dev (= 1.0.8-5build1),
 libc-bin (= 2.39-0ubuntu1),
 libc-dev-bin (= 2.39-0ubuntu1),
 libc6 (= 2.39-0ubuntu1),
 libc6-dev (= 2.39-0ubuntu1),
 libcap-ng0 (= 0.8.4-2),
 libcap2 (= 1:2.66-4ubuntu1),
 libcc1-0 (= 14-20240201-3ubuntu1),
 libcom-err2 (= 1.47.0-2ubuntu1),
 libcrypt-dev (= 1:4.4.36-4),
 libcrypt1 (= 1:4.4.36-4),
 libctf-nobfd0 (= 2.42-2ubuntu1),
 libctf0 (= 2.42-2ubuntu1),
 libcurl3-gnutls (= 8.5.0-2ubuntu2),
 libcurl4-gnutls-dev (= 8.5.0-2ubuntu2),
 libdb5.3 (= 5.3.28+dfsg2-4),
 libdebconfclient0 (= 0.271ubuntu1),
 libdebhelper-perl (= 13.13ubuntu1),
 libdeflate-dev (= 1.19-1),
 libdeflate0 (= 1.19-1),
 libdpkg-perl (= 1.22.4ubuntu3),
 libdw1 (= 0.190-1),
 libelf1 (= 0.190-1),
 libffi8 (= 3.4.4-2),
 libfile-stripnondeterminism-perl (= 1.13.1-1),
 libgcc-13-dev (= 13.2.0-13ubuntu1),
 libgcc-s1 (= 14-20240201-3ubuntu1),
 libgcrypt20 (= 1.10.3-2),
 libgdbm-compat4 (= 1.23-5),
 libgdbm6 (= 1.23-5),
 libgmp10 (= 2:6.3.0+dfsg-2ubuntu4),
 libgnutls30 (= 3.8.3-1ubuntu1),
 libgomp1 (= 14-20240201-3ubuntu1),
 libgpg-error0 (= 1.47-3build1),
 libgssapi-krb5-2 (= 1.20.1-5build1),
 libhogweed6 (= 3.9.1-2),
 libhts-dev (= 1.18+ds-1),
 libhts3 (= 1.18+ds-1),
 libhtscodecs2 (= 1.6.0-1),
 libicu74 (= 74.2-1ubuntu1),
 libidn2-0 (= 2.3.7-2),
 libio-pty-perl (= 1:1.20-1),
 libisl23 (= 0.26-3),
 libjansson4 (= 2.14-2),
 libk5crypto3 (= 1.20.1-5build1),
 libkeyutils1 (= 1.6.3-3),
 libkrb5-3 (= 1.20.1-5build1),
 libkrb5support0 (= 1.20.1-5build1),
 libldap2 (= 2.6.7+dfsg-1~exp1ubuntu1),
 liblz4-1 (= 1.9.4-1),
 liblzma-dev (= 5.4.5-0.3),
 liblzma5 (= 5.4.5-0.3),
 libmagic-mgc (= 1:5.45-2),
 libmagic1 (= 1:5.45-2),
 libmd0 (= 1.1.0-2),
 libmount1 (= 2.39.2-6ubuntu1),
 libmpc3 (= 1.3.1-1),
 libmpfr6 (= 4.2.1-1),
 libncurses-dev (= 6.4+20240113-1ubuntu1),
 libncurses6 (= 6.4+20240113-1ubuntu1),
 libncursesw6 (= 6.4+20240113-1ubuntu1),
 libnettle8 (= 3.9.1-2),
 libnghttp2-14 (= 1.59.0-1),
 libnsl-dev (= 1.3.0-3),
 libnsl2 (= 1.3.0-3),
 libp11-kit0 (= 0.25.3-4ubuntu1),
 libpam-modules (= 1.5.2-9.1ubuntu2),
 libpam-modules-bin (= 1.5.2-9.1ubuntu2),
 libpam-runtime (= 1.5.2-9.1ubuntu2),
 libpam0g (= 1.5.2-9.1ubuntu2),
 libpcre2-8-0 (= 10.42-4ubuntu1),
 libperl5.38 (= 5.38.2-3),
 libpipeline1 (= 1.5.7-1),
 libpkgconf3 (= 1.8.1-2),
 libpsl5 (= 0.21.2-1build1),
 librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4),
 libsasl2-2 (= 2.1.28+dfsg1-4),
 libsasl2-modules-db (= 2.1.28+dfsg1-4),
 libseccomp2 (= 2.5.5-1ubuntu1),
 libselinux1 (= 3.5-2build1),
 libsframe1 (= 2.42-2ubuntu1),
 libsmartcols1 (= 2.39.2-6ubuntu1),
 libssh-4 (= 0.10.6-2),
 libssl3 (= 3.0.10-1ubuntu4),
 libstdc++-13-dev (= 13.2.0-13ubuntu1),
 libstdc++6 (= 14-20240201-3ubuntu1),
 libsub-override-perl (= 0.10-1),
 libsystemd0 (= 255.2-3ubuntu2),
 libtasn1-6 (= 4.19.0-3),
 libtinfo6 (= 6.4+20240113-1ubuntu1),
 libtirpc-common (= 1.3.4+ds-1build1),
 libtirpc-dev (= 1.3.4+ds-1build1),
 libtirpc3 (= 1.3.4+ds-1build1),
 libtool (= 2.4.7-7),
 libubsan1 (= 14-20240201-3ubuntu1),
 libuchardet0 (= 0.0.8-1),
 libudev1 (= 255.2-3ubuntu2),
 libunistring5 (= 1.1-2),
 libuuid1 (= 2.39.2-6ubuntu1),
 libxml2 (= 2.9.14+dfsg-1.3ubuntu1),
 libzstd1 (= 1.5.5+dfsg2-2),
 linux-libc-dev (= 6.8.0-11.11),
 login (= 1:4.13+dfsg1-3ubuntu1),
 lto-disabled-list (= 46),
 m4 (= 1.4.19-4),
 make (= 4.3-4.1build1),
 man-db (= 2.12.0-3),
 mawk (= 1.3.4.20240123-1),
 ncurses-base (= 6.4+20240113-1ubuntu1),
 ncurses-bin (= 6.4+20240113-1ubuntu1),
 patch (= 2.7.6-7build2),
 perl (= 5.38.2-3),
 perl-base (= 5.38.2-3),
 perl-modules-5.38 (= 5.38.2-3),
 pkgconf (= 1.8.1-2),
 pkgconf-bin (= 1.8.1-2),
 po-debconf (= 1.0.21+nmu1),
 rpcsvc-proto (= 1.4.2-0ubuntu6),
 sed (= 4.9-2),
 sensible-utils (= 0.0.22),
 sysvinit-utils (= 3.08-3ubuntu1),
 tabix (= 1.18+ds-1),
 tar (= 1.35+dfsg-3),
 util-linux (= 2.39.2-6ubuntu1),
 xz-utils (= 5.4.5-0.3),
 zlib1g (= 1:1.3.dfsg-3ubuntu1),
 zlib1g-dev (= 1:1.3.dfsg-3ubuntu1)
Environment:
 DEB_BUILD_OPTIONS="parallel=4"
 DEB_BUILD_PROFILES="noudeb"
 LANG="C.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1708190561"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


samtools_1.19.2-1_armhf.deb
---------------------------

 new Debian package, version 2.0.
 size 601904 bytes: control archive=2921 bytes.
     915 bytes,    18 lines      control
    5605 bytes,    82 lines      md5sums
 Package: samtools
 Version: 1.19.2-1
 Architecture: armhf
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1129
 Depends: libc6 (>= 2.34), libhts3 (>= 1.17), libncurses6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.2.3.3)
 Suggests: cwltool
 Section: science
 Priority: optional
 Homepage: https://www.htslib.org/
 Description: processing sequence alignments in SAM, BAM and CRAM formats
  Samtools is a set of utilities that manipulate nucleotide sequence alignments
  in the binary BAM format. It imports from and exports to the ascii SAM
  (Sequence Alignment/Map) and CRAM formats, does sorting, merging and indexing,
  and allows one to retrieve reads in any regions swiftly. It is designed to work
  on a stream, and is able to open a BAM or CRAM (not SAM) file on a remote FTP
  or HTTP server.

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drwxr-xr-x root/root         0 2024-02-17 17:22 ./usr/bin/
-rwxr-xr-x root/root     13868 2024-02-17 17:22 ./usr/bin/ace2sam
-rwxr-xr-x root/root      5443 2024-02-17 17:22 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root      3360 2024-02-17 17:22 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root     17996 2024-02-17 17:22 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root      3300 2024-02-17 17:22 ./usr/bin/fasta-sanitize.pl
-rwxr-xr-x root/root      6121 2024-02-17 17:22 ./usr/bin/interpolate_sam.pl
-rwxr-xr-x root/root      9772 2024-02-17 17:22 ./usr/bin/maq2sam-long
-rwxr-xr-x root/root      9772 2024-02-17 17:22 ./usr/bin/maq2sam-short
-rwxr-xr-x root/root      9772 2024-02-17 17:22 ./usr/bin/md5fa
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-rwxr-xr-x root/root      7969 2024-02-17 17:22 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root     44331 2024-02-17 17:22 ./usr/bin/plot-ampliconstats
-rwxr-xr-x root/root     55292 2024-02-17 17:22 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root      3204 2024-02-17 17:22 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root      8957 2024-02-17 17:22 ./usr/bin/sam2vcf.pl
-rwxr-xr-x root/root    520936 2024-02-17 17:22 ./usr/bin/samtools
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-rwxr-xr-x root/root     11333 2024-02-17 17:22 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root      3905 2024-02-17 17:22 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root     18004 2024-02-17 17:22 ./usr/bin/wgsim
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-rwxr-xr-x root/root      3579 2024-02-17 17:22 ./usr/bin/zoom2sam.pl
drwxr-xr-x root/root         0 2024-02-17 17:22 ./usr/share/
drwxr-xr-x root/root         0 2024-02-17 17:22 ./usr/share/commonwl/
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drwxr-xr-x root/root         0 2024-02-17 17:22 ./usr/share/doc/
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-rw-r--r-- root/root       828 2024-01-24 09:34 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root       497 2023-12-15 15:06 ./usr/share/doc/samtools/README.Debian
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-rw-r--r-- root/root      2250 2024-02-17 17:08 ./usr/share/doc/samtools/copyright
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drwxr-xr-x root/root         0 2024-02-17 17:22 ./usr/share/man/man1/
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+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
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Purging /<<BUILDDIR>>
Not removing build depends: as requested

+------------------------------------------------------------------------------+
| Summary                                                                      |
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Build Architecture: armhf
Build Type: any
Build-Space: 30284
Build-Time: 62
Distribution: noble-proposed
Host Architecture: armhf
Install-Time: 9
Job: samtools_1.19.2-1.dsc
Machine Architecture: arm64
Package: samtools
Package-Time: 73
Source-Version: 1.19.2-1
Space: 30284
Status: successful
Version: 1.19.2-1
--------------------------------------------------------------------------------
Finished at 2024-02-18T05:20:05Z
Build needed 00:01:13, 30284k disk space
RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27788433
Scanning for processes to kill in build PACKAGEBUILD-27788433