samtools →
1.19-1 →
armhf → 2023-12-18 06:26:43
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| samtools 1.19-1 (armhf) Mon, 18 Dec 2023 06:24:50 +0000 |
+==============================================================================+
Package: samtools
Version: 1.19-1
Source Version: 1.19-1
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-c4b16a4b-8add-4063-a785-f05795f86387' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/samtools-iQY3TG/resolver-VKeXY7' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.3 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.0 MB]
Fetched 29.3 MB in 5s (5594 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/samtools.git
Please use:
git clone https://salsa.debian.org/med-team/samtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 5688 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main samtools 1.19-1 (dsc) [2284 B]
Get:2 http://172.17.4.1/private trixie-staging/main samtools 1.19-1 (tar) [5664 kB]
Get:3 http://172.17.4.1/private trixie-staging/main samtools 1.19-1 (diff) [21.7 kB]
Fetched 5688 kB in 1s (7870 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/samtools-iQY3TG/samtools-1.19' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/samtools-iQY3TG' 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, pkg-config, 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, pkg-config, 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 [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [784 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [805 B]
Fetched 2198 B in 0s (0 B/s)
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 additional packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev bash-completion
bsdextrautils bsdutils debhelper dh-autoreconf dh-strip-nondeterminism
dpkg-dev dwz file gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libblkid1 libbrotli1 libbz2-dev libcurl3-gnutls
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0
libdpkg-perl libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3
libhtscodecs2 libicu72 libio-pty-perl liblzma-dev liblzma5 libmagic-mgc
libmagic1 libmount1 libncurses-dev libncurses6 libncursesw6 libnghttp2-14
libpipeline1 libpkgconf3 libpsl5 librtmp1 libsmartcols1 libssh2-1
libsub-override-perl libtinfo6 libtool libuchardet0 libuuid1 libxml2 m4
man-db mount ncurses-base ncurses-bin pkg-config pkgconf pkgconf-bin
po-debconf sensible-utils tabix util-linux xz-utils zlib1g-dev
Suggested packages:
gnu-standards autoconf-doc dh-make debian-keyring gettext-doc
libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev
libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev git bzr
liblzma-doc cryptsetup-bin ncurses-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser nfs-common
libmail-box-perl dosfstools kbd util-linux-extra util-linux-locales
Recommended packages:
libalgorithm-merge-perl curl | wget | lynx bzip2-doc ca-certificates
libfile-fcntllock-perl libarchive-cpio-perl libgpm2 publicsuffix libltdl-dev
uuid-runtime libmail-sendmail-perl
The following NEW packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev bash-completion
bsdextrautils debhelper 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 libelf1 libfile-stripnondeterminism-perl
libhts-dev libhts3 libhtscodecs2 libicu72 libio-pty-perl liblzma-dev
libmagic-mgc libmagic1 libncurses-dev libncurses6 libnghttp2-14 libpipeline1
libpkgconf3 libpsl5 librtmp1 libssh2-1 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db pkg-config pkgconf pkgconf-bin po-debconf
sbuild-build-depends-main-dummy sensible-utils tabix zlib1g-dev
The following packages will be upgraded:
bsdutils dpkg-dev libblkid1 libdpkg-perl liblzma5 libmount1 libncursesw6
libsmartcols1 libtinfo6 libuuid1 mount ncurses-base ncurses-bin util-linux
xz-utils
15 upgraded, 56 newly installed, 0 to remove and 61 not upgraded.
1 not fully installed or removed.
Need to get 28.4 MB/30.4 MB of archives.
After this operation, 94.7 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [960 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf mount armhf 2.39.3-2 [134 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf bsdutils armhf 1:2.39.3-2 [86.6 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf ncurses-bin armhf 6.4+20231209-1 [422 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf util-linux armhf 2.39.3-2 [1113 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf ncurses-base all 6.4+20231209-1 [267 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf autoconf-archive all 20220903-3 [775 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libblkid1 armhf 2.39.3-2 [145 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf liblzma5 armhf 5.4.5-0.1 [226 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf libmount1 armhf 2.39.3-2 [168 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf libtinfo6 armhf 6.4+20231209-1 [325 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf libncursesw6 armhf 6.4+20231209-1 [107 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf libsmartcols1 armhf 2.39.3-2 [102 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf libuuid1 armhf 2.39.3-2 [28.2 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-2 [81.2 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-1 [1358 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf bash-completion all 1:2.11-8 [224 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf xz-utils armhf 5.4.5-0.1 [499 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.8 [82.1 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.8 [956 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.1.0-2 [280 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.58.0-1 [61.7 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-3 [195 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 8.4.0-2+rpi1 [358 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libcurl4-gnutls-dev armhf 8.4.0-2+rpi1 [441 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf libdeflate-dev armhf 1.18-1 [45.8 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libhtscodecs2 armhf 1.5.2-1 [60.0 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf libhts3 armhf 1.18+ds-1 [380 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf liblzma-dev armhf 5.4.5-0.1 [278 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libhts-dev armhf 1.18+ds-1 [1539 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf libio-pty-perl armhf 1:1.17-1 [34.7 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libncurses6 armhf 6.4+20231209-1 [80.5 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libncurses-dev armhf 6.4+20231209-1 [290 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf pkgconf-bin armhf 1.8.1-1 [27.8 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf pkgconf armhf 1.8.1-1 [25.9 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf pkg-config armhf 1.8.1-1 [13.7 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf tabix armhf 1.18+ds-1 [380 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 28.4 MB in 4s (7615 kB/s)
(Reading database ... 12577 files and directories currently installed.)
Preparing to unpack .../mount_2.39.3-2_armhf.deb ...
Unpacking mount (2.39.3-2) over (2.39.2-5) ...
Preparing to unpack .../bsdutils_1%3a2.39.3-2_armhf.deb ...
Unpacking bsdutils (1:2.39.3-2) over (1:2.39.2-5) ...
Setting up bsdutils (1:2.39.3-2) ...
(Reading database ... 12577 files and directories currently installed.)
Preparing to unpack .../ncurses-bin_6.4+20231209-1_armhf.deb ...
Unpacking ncurses-bin (6.4+20231209-1) over (6.4+20231016-1) ...
Setting up ncurses-bin (6.4+20231209-1) ...
(Reading database ... 12577 files and directories currently installed.)
Preparing to unpack .../util-linux_2.39.3-2_armhf.deb ...
Unpacking util-linux (2.39.3-2) over (2.39.2-5) ...
Setting up util-linux (2.39.3-2) ...
(Reading database ... 12578 files and directories currently installed.)
Preparing to unpack .../ncurses-base_6.4+20231209-1_all.deb ...
Unpacking ncurses-base (6.4+20231209-1) over (6.4+20231016-1) ...
Setting up ncurses-base (6.4+20231209-1) ...
Selecting previously unselected package autoconf-archive.
(Reading database ... 12578 files and directories currently installed.)
Preparing to unpack .../autoconf-archive_20220903-3_all.deb ...
Unpacking autoconf-archive (20220903-3) ...
Preparing to unpack .../libblkid1_2.39.3-2_armhf.deb ...
Unpacking libblkid1:armhf (2.39.3-2) over (2.39.2-5) ...
Setting up libblkid1:armhf (2.39.3-2) ...
(Reading database ... 13760 files and directories currently installed.)
Preparing to unpack .../liblzma5_5.4.5-0.1_armhf.deb ...
Unpacking liblzma5:armhf (5.4.5-0.1) over (5.4.4-0.1) ...
Setting up liblzma5:armhf (5.4.5-0.1) ...
(Reading database ... 13760 files and directories currently installed.)
Preparing to unpack .../libmount1_2.39.3-2_armhf.deb ...
Unpacking libmount1:armhf (2.39.3-2) over (2.39.2-5) ...
Setting up libmount1:armhf (2.39.3-2) ...
(Reading database ... 13760 files and directories currently installed.)
Preparing to unpack .../libtinfo6_6.4+20231209-1_armhf.deb ...
Unpacking libtinfo6:armhf (6.4+20231209-1) over (6.4+20231016-1) ...
Setting up libtinfo6:armhf (6.4+20231209-1) ...
(Reading database ... 13760 files and directories currently installed.)
Preparing to unpack .../libncursesw6_6.4+20231209-1_armhf.deb ...
Unpacking libncursesw6:armhf (6.4+20231209-1) over (6.4+20231016-1) ...
Setting up libncursesw6:armhf (6.4+20231209-1) ...
(Reading database ... 13760 files and directories currently installed.)
Preparing to unpack .../libsmartcols1_2.39.3-2_armhf.deb ...
Unpacking libsmartcols1:armhf (2.39.3-2) over (2.39.2-5) ...
Setting up libsmartcols1:armhf (2.39.3-2) ...
(Reading database ... 13760 files and directories currently installed.)
Preparing to unpack .../libuuid1_2.39.3-2_armhf.deb ...
Unpacking libuuid1:armhf (2.39.3-2) over (2.39.2-5) ...
Setting up libuuid1:armhf (2.39.3-2) ...
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 13760 files and directories currently installed.)
Preparing to unpack .../00-libuchardet0_0.0.8-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.8-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../01-groff-base_1.23.0-3_armhf.deb ...
Unpacking groff-base (1.23.0-3) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../02-bsdextrautils_2.39.3-2_armhf.deb ...
Unpacking bsdextrautils (2.39.3-2) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../03-libpipeline1_1.5.7-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.12.0-1_armhf.deb ...
Unpacking man-db (2.12.0-1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../05-sensible-utils_0.0.20_all.deb ...
Unpacking sensible-utils (0.0.20) ...
Selecting previously unselected package bash-completion.
Preparing to unpack .../06-bash-completion_1%3a2.11-8_all.deb ...
Unpacking bash-completion (1:2.11-8) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../07-libmagic-mgc_1%3a5.45-2_armhf.deb ...
Unpacking libmagic-mgc (1:5.45-2) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../08-libmagic1_1%3a5.45-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.45-2) ...
Selecting previously unselected package file.
Preparing to unpack .../09-file_1%3a5.45-2_armhf.deb ...
Unpacking file (1:5.45-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../10-gettext-base_0.21-14_armhf.deb ...
Unpacking gettext-base (0.21-14) ...
Preparing to unpack .../11-xz-utils_5.4.5-0.1_armhf.deb ...
Unpacking xz-utils (5.4.5-0.1) over (5.4.4-0.1) ...
Selecting previously unselected package m4.
Preparing to unpack .../12-m4_1.4.19-4_armhf.deb ...
Unpacking m4 (1.4.19-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../13-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../16-autopoint_0.21-14_all.deb ...
Unpacking autopoint (0.21-14) ...
Preparing to unpack .../17-dpkg-dev_1.22.1+rpi1_all.deb ...
Unpacking dpkg-dev (1.22.1+rpi1) over (1.22.0+rpi1) ...
Preparing to unpack .../18-libdpkg-perl_1.22.1+rpi1_all.deb ...
Unpacking libdpkg-perl (1.22.1+rpi1) over (1.22.0+rpi1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../19-libdebhelper-perl_13.11.8_all.deb ...
Unpacking libdebhelper-perl (13.11.8) ...
Selecting previously unselected package libtool.
Preparing to unpack .../20-libtool_2.4.7-7_all.deb ...
Unpacking libtool (2.4.7-7) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../21-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../22-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../23-libsub-override-perl_0.10-1_all.deb ...
Unpacking libsub-override-perl (0.10-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../24-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../25-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../26-libelf1_0.188-2.1+rpi1_armhf.deb ...
Unpacking libelf1:armhf (0.188-2.1+rpi1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../27-dwz_0.15-1_armhf.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:armhf.
Preparing to unpack .../28-libicu72_72.1-4_armhf.deb ...
Unpacking libicu72:armhf (72.1-4) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../29-libxml2_2.9.14+dfsg-1.3_armhf.deb ...
Unpacking libxml2:armhf (2.9.14+dfsg-1.3) ...
Selecting previously unselected package gettext.
Preparing to unpack .../30-gettext_0.21-14_armhf.deb ...
Unpacking gettext (0.21-14) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../31-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../32-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../33-debhelper_13.11.8_all.deb ...
Unpacking debhelper (13.11.8) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../34-libbrotli1_1.1.0-2_armhf.deb ...
Unpacking libbrotli1:armhf (1.1.0-2) ...
Selecting previously unselected package libbz2-dev:armhf.
Preparing to unpack .../35-libbz2-dev_1.0.8-5+b2_armhf.deb ...
Unpacking libbz2-dev:armhf (1.0.8-5+b2) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../36-libnghttp2-14_1.58.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.58.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../37-libpsl5_0.21.2-1+b1_armhf.deb ...
Unpacking libpsl5:armhf (0.21.2-1+b1) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../38-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../39-libssh2-1_1.11.0-3_armhf.deb ...
Unpacking libssh2-1:armhf (1.11.0-3) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../40-libcurl3-gnutls_8.4.0-2+rpi1_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (8.4.0-2+rpi1) ...
Selecting previously unselected package libcurl4-gnutls-dev:armhf.
Preparing to unpack .../41-libcurl4-gnutls-dev_8.4.0-2+rpi1_armhf.deb ...
Unpacking libcurl4-gnutls-dev:armhf (8.4.0-2+rpi1) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../42-libdeflate0_1.18-1_armhf.deb ...
Unpacking libdeflate0:armhf (1.18-1) ...
Selecting previously unselected package libdeflate-dev:armhf.
Preparing to unpack .../43-libdeflate-dev_1.18-1_armhf.deb ...
Unpacking libdeflate-dev:armhf (1.18-1) ...
Selecting previously unselected package libhtscodecs2:armhf.
Preparing to unpack .../44-libhtscodecs2_1.5.2-1_armhf.deb ...
Unpacking libhtscodecs2:armhf (1.5.2-1) ...
Selecting previously unselected package libhts3:armhf.
Preparing to unpack .../45-libhts3_1.18+ds-1_armhf.deb ...
Unpacking libhts3:armhf (1.18+ds-1) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../46-liblzma-dev_5.4.5-0.1_armhf.deb ...
Unpacking liblzma-dev:armhf (5.4.5-0.1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../47-zlib1g-dev_1%3a1.2.13.dfsg-3_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.13.dfsg-3) ...
Selecting previously unselected package libhts-dev:armhf.
Preparing to unpack .../48-libhts-dev_1.18+ds-1_armhf.deb ...
Unpacking libhts-dev:armhf (1.18+ds-1) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../49-libio-pty-perl_1%3a1.17-1_armhf.deb ...
Unpacking libio-pty-perl (1:1.17-1) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../50-libncurses6_6.4+20231209-1_armhf.deb ...
Unpacking libncurses6:armhf (6.4+20231209-1) ...
Selecting previously unselected package libncurses-dev:armhf.
Preparing to unpack .../51-libncurses-dev_6.4+20231209-1_armhf.deb ...
Unpacking libncurses-dev:armhf (6.4+20231209-1) ...
Selecting previously unselected package libpkgconf3:armhf.
Preparing to unpack .../52-libpkgconf3_1.8.1-1_armhf.deb ...
Unpacking libpkgconf3:armhf (1.8.1-1) ...
Selecting previously unselected package pkgconf-bin.
Preparing to unpack .../53-pkgconf-bin_1.8.1-1_armhf.deb ...
Unpacking pkgconf-bin (1.8.1-1) ...
Selecting previously unselected package pkgconf:armhf.
Preparing to unpack .../54-pkgconf_1.8.1-1_armhf.deb ...
Unpacking pkgconf:armhf (1.8.1-1) ...
Selecting previously unselected package pkg-config:armhf.
Preparing to unpack .../55-pkg-config_1.8.1-1_armhf.deb ...
Unpacking pkg-config:armhf (1.8.1-1) ...
Selecting previously unselected package tabix.
Preparing to unpack .../56-tabix_1.18+ds-1_armhf.deb ...
Unpacking tabix (1.18+ds-1) ...
Selecting previously unselected package sbuild-build-depends-main-dummy.
Preparing to unpack .../57-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up libhtscodecs2:armhf (1.5.2-1) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up libpsl5:armhf (0.21.2-1+b1) ...
Setting up libicu72:armhf (72.1-4) ...
Setting up bsdextrautils (2.39.3-2) ...
Setting up libio-pty-perl (1:1.17-1) ...
Setting up libmagic-mgc (1:5.45-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.8) ...
Setting up libbrotli1:armhf (1.1.0-2) ...
Setting up libnghttp2-14:armhf (1.58.0-1) ...
Setting up libmagic1:armhf (1:5.45-2) ...
Setting up libdeflate0:armhf (1.18-1) ...
Setting up gettext-base (0.21-14) ...
Setting up m4 (1.4.19-4) ...
Setting up autoconf-archive (20220903-3) ...
Setting up file (1:5.45-2) ...
Setting up autotools-dev (20220109.1) ...
Setting up libpkgconf3:armhf (1.8.1-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up bash-completion (1:2.11-8) ...
Setting up libncurses6:armhf (6.4+20231209-1) ...
Setting up xz-utils (5.4.5-0.1) ...
Setting up autopoint (0.21-14) ...
Setting up pkgconf-bin (1.8.1-1) ...
Setting up libdpkg-perl (1.22.1+rpi1) ...
Setting up autoconf (2.71-3) ...
Setting up liblzma-dev:armhf (5.4.5-0.1) ...
Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-3) ...
Setting up mount (2.39.3-2) ...
Setting up sensible-utils (0.0.20) ...
Setting up libuchardet0:armhf (0.0.8-1) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up libssh2-1:armhf (1.11.0-3) ...
Setting up libdeflate-dev:armhf (1.18-1) ...
Setting up tabix (1.18+ds-1) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up libbz2-dev:armhf (1.0.8-5+b2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up libncurses-dev:armhf (6.4+20231209-1) ...
Setting up gettext (0.21-14) ...
Setting up libtool (2.4.7-7) ...
Setting up libcurl3-gnutls:armhf (8.4.0-2+rpi1) ...
Setting up libcurl4-gnutls-dev:armhf (8.4.0-2+rpi1) ...
Setting up dpkg-dev (1.22.1+rpi1) ...
Setting up pkgconf:armhf (1.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up pkg-config:armhf (1.8.1-1) ...
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 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 (2.12.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.11.8) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc-12_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 autoconf-archive_20220903-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.2 bash_5.2.15-2 bash-completion_1:2.11-8 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-2 bsdutils_1:2.39.3-2 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-10+rpi1 cpp-13_13.2.0-5+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.8 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.3.0-10+rpi1 gcc-12-base_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 gcc-13-base_13.2.0-5+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-14 gettext-base_0.21-14 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan8_13.2.0-5+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-5+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-6+rpi1 libblkid1_2.39.3-2 libbrotli1_1.1.0-2 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcc1-0_13.2.0-5+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libcurl3-gnutls_8.4.0-2+rpi1 libcurl4-gnutls-dev_8.4.0-2+rpi1 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.271 libdebhelper-perl_13.11.8 libdeflate-dev_1.18-1 libdeflate0_1.18-1 libdpkg-perl_1.22.1+rpi1 libelf1_0.188-2.1+rpi1 libext2fs2_1.47.0-2 libfakeroot_1.32.1-1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-10+rpi1 libgcc-13-dev_13.2.0-5+rpi1 libgcc-s1_13.2.0-5+rpi1 libgcrypt20_1.10.2-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.1-4 libgomp1_13.2.0-5+rpi1 libgpg-error0_1.47-2 libgssapi-krb5-2_1.20.1-4 libhogweed6_3.9.1-2 libhts-dev_1.18+ds-1 libhts3_1.18+ds-1 libhtscodecs2_1.5.2-1 libicu72_72.1-4 libidn2-0_2.3.4-1 libio-pty-perl_1:1.17-1 libisl23_0.26-3 libjansson4_2.14-2 libk5crypto3_1.20.1-4 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-4 libkrb5support0_1.20.1-4 libksba8_1.6.4-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblocale-gettext-perl_1.07-6 liblz4-1_1.9.4-1+rpi1+b1 liblzma-dev_5.4.5-0.1 liblzma5_5.4.5-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.3-2 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncurses-dev_6.4+20231209-1 libncurses6_6.4+20231209-1 libncursesw6_6.4+20231209-1 libnettle8_3.9.1-2 libnghttp2-14_1.58.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.25.0-5 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libperl5.36_5.36.0-9 libpipeline1_1.5.7-1 libpkgconf3_1.8.1-1 libpsl5_0.21.2-1+b1 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-1 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.3-2 libsqlite3-0_3.43.2-1 libss2_1.47.0-2 libssh2-1_1.11.0-3 libssl3_3.0.11-1 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 libsub-override-perl_0.10-1 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-iconv-perl_1.7-8 libtinfo6_6.4+20231209-1 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-5+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring5_1.1-2 libuuid1_2.39.3-2 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-1 mawk_1.3.4.20230808-1 mount_2.39.3-2 ncurses-base_6.4+20231209-1 ncurses-bin_6.4+20231209-1 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-9 perl-base_5.36.0-9 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 pkg-config_1.8.1-1 pkgconf_1.8.1-1 pkgconf-bin_1.8.1-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.08-3 tabix_1.18+ds-1 tar_1.34+dfsg-1.2 tzdata_2023c-10 usr-is-merged_37 util-linux_2.39.3-2 xz-utils_5.4.5-0.1 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: samtools
Binary: samtools, samtools-test
Architecture: any all
Version: 1.19-1
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, pkg-config, tabix, liblzma-dev, libbz2-dev
Package-List:
samtools deb science optional arch=any
samtools-test deb science optional arch=all
Checksums-Sha1:
10709035bb45ef8f210a40515eb3377ff297db8d 5663728 samtools_1.19.orig.tar.gz
c2138fc66b17941bdeae982150c64933e5a016fa 21708 samtools_1.19-1.debian.tar.xz
Checksums-Sha256:
b068f1eb1fcad8bd90296f60ebf3e67343cd076afb004d68bd75525f95218db2 5663728 samtools_1.19.orig.tar.gz
af8b22fcef8d24d54f489bebc1630ad30550ffb0cdf07d823f63bc9876cbbdfa 21708 samtools_1.19-1.debian.tar.xz
Files:
7d0222ae739a65a9a0c0041cdafdc5a7 5663728 samtools_1.19.orig.tar.gz
0c2ae5210856fd1563061d6c6648bdb4 21708 samtools_1.19-1.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=NFF/
-----END PGP SIGNATURE-----
gpgv: Signature made Fri Dec 15 16:40:58 2023 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_1.19-1.dsc: no acceptable signature found
dpkg-source: info: extracting samtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking samtools_1.19.orig.tar.gz
dpkg-source: info: unpacking samtools_1.19-1.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=en_GB.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=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-c4b16a4b-8add-4063-a785-f05795f86387
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package samtools
dpkg-buildpackage: info: source version 1.19-1
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/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 \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
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... /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 -fstack-clash-protection -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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"' > version.h
echo '#define SAMTOOLS_CC "gcc"' >> version.h
echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h
echo '#define SAMTOOLS_CFLAGS "-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security"' >> version.h
echo '#define SAMTOOLS_LDFLAGS "-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
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fstack-clash-protection -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -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,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz
gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz
gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz
gcc -L./lz4 -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,-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,-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,-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,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread
gcc -L./lz4 -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,-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,-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,-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/NpRJZyXrXA/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 979200 -s 6 /tmp/NpRJZyXrXA/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 652804 -s 6 /tmp/NpRJZyXrXA/bgzip.dat.gz
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/NpRJZyXrXA/faidx.fa 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/NpRJZyXrXA/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/NpRJZyXrXA/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/NpRJZyXrXA/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/NpRJZyXrXA/faidx.fa 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/NpRJZyXrXA/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/NpRJZyXrXA/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/NpRJZyXrXA/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/NpRJZyXrXA/fqidx.fq 3:11-13
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/NpRJZyXrXA/fqidx.fq.gz 3:11-13
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/NpRJZyXrXA/fqidx.fq 2:998-1003
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/NpRJZyXrXA/fqidx.fq.gz 2:998-1003
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/NpRJZyXrXA/fqidx.fq 1:100-104
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/NpRJZyXrXA/fqidx.fq.gz 1:100-104
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/NpRJZyXrXA/fqidx.fq 1:99998-100007
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/NpRJZyXrXA/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/NpRJZyXrXA/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/NpRJZyXrXA/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view /tmp/NpRJZyXrXA/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/NpRJZyXrXA/test_input_1_b.bam.bai ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/NpRJZyXrXA/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/NpRJZyXrXA/test_input_1_b.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/NpRJZyXrXA/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/NpRJZyXrXA/auto_indexed.csi && cat /tmp/NpRJZyXrXA/auto_indexed.csi
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.cram /tmp/NpRJZyXrXA/auto_indexed.crai && cat /tmp/NpRJZyXrXA/auto_indexed.crai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.sam /tmp/NpRJZyXrXA/auto_indexed.csi && cat /tmp/NpRJZyXrXA/auto_indexed.csi
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/NpRJZyXrXA/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/NpRJZyXrXA/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/NpRJZyXrXA/test_input_1_b.bam.bai ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/NpRJZyXrXA/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/NpRJZyXrXA/test_input_1_b.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 -X /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /tmp/NpRJZyXrXA/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/NpRJZyXrXA/auto_indexed.csi && cat /tmp/NpRJZyXrXA/auto_indexed.csi
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.cram /tmp/NpRJZyXrXA/auto_indexed.crai && cat /tmp/NpRJZyXrXA/auto_indexed.crai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.sam /tmp/NpRJZyXrXA/auto_indexed.csi && cat /tmp/NpRJZyXrXA/auto_indexed.csi
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/NpRJZyXrXA/mpileup.bam.list -f /tmp/NpRJZyXrXA/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/NpRJZyXrXA/mpileup.cram.list -f /tmp/NpRJZyXrXA/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/NpRJZyXrXA/mpileup.bam.urllist -f /tmp/NpRJZyXrXA/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/NpRJZyXrXA/mpileup.cram.urllist -f /tmp/NpRJZyXrXA/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/NpRJZyXrXA/mpileup.ref.fa.gz -r17:1050-1060 /tmp/NpRJZyXrXA/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/NpRJZyXrXA/mpileup.ref.fa.gz -r17:1050-1060 /tmp/NpRJZyXrXA/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/NpRJZyXrXA/view.001.fogn (SAM input) .. ok
50: Count -R /tmp/NpRJZyXrXA/view.001.fogn (SAM input) .. ok
51: Filter -R /tmp/NpRJZyXrXA/view.001.fogn (BAM input) .. ok
52: Count -R /tmp/NpRJZyXrXA/view.001.fogn (BAM input) .. ok
53: Filter -R /tmp/NpRJZyXrXA/view.001.fogn (CRAM input) .. ok
54: Count -R /tmp/NpRJZyXrXA/view.001.fogn (CRAM input) .. ok
55: Filter -R /tmp/NpRJZyXrXA/view.001.fogn -r grp2 (SAM input).. ok
56: Count -R /tmp/NpRJZyXrXA/view.001.fogn -r grp2 (SAM input).. ok
57: Filter -R /tmp/NpRJZyXrXA/view.001.fogn -r grp2 (BAM input).. ok
58: Count -R /tmp/NpRJZyXrXA/view.001.fogn -r grp2 (BAM input).. ok
59: Filter -R /tmp/NpRJZyXrXA/view.001.fogn -r grp2 (CRAM input).. ok
60: Count -R /tmp/NpRJZyXrXA/view.001.fogn -r grp2 (CRAM input).. ok
61: Filter -r grp2 -R /tmp/NpRJZyXrXA/view.001.fogn (SAM input).. ok
62: Count -r grp2 -R /tmp/NpRJZyXrXA/view.001.fogn (SAM input).. ok
63: Filter -r grp2 -R /tmp/NpRJZyXrXA/view.001.fogn (BAM input).. ok
64: Count -r grp2 -R /tmp/NpRJZyXrXA/view.001.fogn (BAM input).. ok
65: Filter -r grp2 -R /tmp/NpRJZyXrXA/view.001.fogn (CRAM input).. ok
66: Count -r grp2 -R /tmp/NpRJZyXrXA/view.001.fogn (CRAM input).. ok
67: Filter -N /tmp/NpRJZyXrXA/view.001.forn (SAM input) .. ok
68: Count -N /tmp/NpRJZyXrXA/view.001.forn (SAM input) .. ok
69: Filter -N /tmp/NpRJZyXrXA/view.001.forn (BAM input) .. ok
70: Count -N /tmp/NpRJZyXrXA/view.001.forn (BAM input) .. ok
71: Filter -N /tmp/NpRJZyXrXA/view.001.forn (CRAM input) .. ok
72: Count -N /tmp/NpRJZyXrXA/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/NpRJZyXrXA/view.001.fobc (SAM input) .. ok
86: Count -D BC:/tmp/NpRJZyXrXA/view.001.fobc (SAM input) .. ok
87: Filter -D BC:/tmp/NpRJZyXrXA/view.001.fobc (BAM input) .. ok
88: Count -D BC:/tmp/NpRJZyXrXA/view.001.fobc (BAM input) .. ok
89: Filter -D BC:/tmp/NpRJZyXrXA/view.001.fobc (CRAM input) .. ok
90: Count -D BC:/tmp/NpRJZyXrXA/view.001.fobc (CRAM input) .. ok
91: Filter -D BC:/tmp/NpRJZyXrXA/view.001.fobc -d BC:TGCA (SAM input).. ok
92: Count -D BC:/tmp/NpRJZyXrXA/view.001.fobc -d BC:TGCA (SAM input).. ok
93: Filter -D BC:/tmp/NpRJZyXrXA/view.001.fobc -d BC:TGCA (BAM input).. ok
94: Count -D BC:/tmp/NpRJZyXrXA/view.001.fobc -d BC:TGCA (BAM input).. ok
95: Filter -D BC:/tmp/NpRJZyXrXA/view.001.fobc -d BC:TGCA (CRAM input).. ok
96: Count -D BC:/tmp/NpRJZyXrXA/view.001.fobc -d BC:TGCA (CRAM input).. ok
97: Filter -d BC:TGCA -D BC:/tmp/NpRJZyXrXA/view.001.fobc (SAM input).. ok
98: Count -d BC:TGCA -D BC:/tmp/NpRJZyXrXA/view.001.fobc (SAM input).. ok
99: Filter -d BC:TGCA -D BC:/tmp/NpRJZyXrXA/view.001.fobc (BAM input).. ok
100: Count -d BC:TGCA -D BC:/tmp/NpRJZyXrXA/view.001.fobc (BAM input).. ok
101: Filter -d BC:TGCA -D BC:/tmp/NpRJZyXrXA/view.001.fobc (CRAM input).. ok
102: Count -d BC:TGCA -D BC:/tmp/NpRJZyXrXA/view.001.fobc (CRAM input).. ok
103: Filter -D RG:/tmp/NpRJZyXrXA/view.001.fogn (SAM input) .. ok
104: Count -D RG:/tmp/NpRJZyXrXA/view.001.fogn (SAM input) .. ok
105: Filter -D RG:/tmp/NpRJZyXrXA/view.001.fogn (BAM input) .. ok
106: Count -D RG:/tmp/NpRJZyXrXA/view.001.fogn (BAM input) .. ok
107: Filter -D RG:/tmp/NpRJZyXrXA/view.001.fogn (CRAM input).. ok
108: Count -D RG:/tmp/NpRJZyXrXA/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/NpRJZyXrXA/view.test115.sam -h -d TGCA /tmp/NpRJZyXrXA/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/NpRJZyXrXA/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/NpRJZyXrXA/view.test117.sam -h -d TGCA /tmp/NpRJZyXrXA/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/NpRJZyXrXA/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/NpRJZyXrXA/view.test119.sam -h -d TGCA /tmp/NpRJZyXrXA/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/NpRJZyXrXA/view.test006.cram --no-PG
.. expected failure
121: Filter -D BClong:/tmp/NpRJZyXrXA/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/NpRJZyXrXA/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/NpRJZyXrXA/view.test121.sam -h -D BClong:/tmp/NpRJZyXrXA/view.001.fobc /tmp/NpRJZyXrXA/view.001.sam --no-PG
.. expected failure
122: Count -D BClong:/tmp/NpRJZyXrXA/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/NpRJZyXrXA/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/NpRJZyXrXA/view.001.fobc /tmp/NpRJZyXrXA/view.001.sam --no-PG
.. expected failure
123: Filter -D BClong:/tmp/NpRJZyXrXA/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/NpRJZyXrXA/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/NpRJZyXrXA/view.test123.sam -h -D BClong:/tmp/NpRJZyXrXA/view.001.fobc /tmp/NpRJZyXrXA/view.test001.bam --no-PG
.. expected failure
124: Count -D BClong:/tmp/NpRJZyXrXA/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/NpRJZyXrXA/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/NpRJZyXrXA/view.001.fobc /tmp/NpRJZyXrXA/view.test001.bam --no-PG
.. expected failure
125: Filter -D BClong:/tmp/NpRJZyXrXA/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/NpRJZyXrXA/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/NpRJZyXrXA/view.test125.sam -h -D BClong:/tmp/NpRJZyXrXA/view.001.fobc /tmp/NpRJZyXrXA/view.test006.cram --no-PG
.. expected failure
126: Count -D BClong:/tmp/NpRJZyXrXA/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/NpRJZyXrXA/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/NpRJZyXrXA/view.001.fobc /tmp/NpRJZyXrXA/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/NpRJZyXrXA/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/NpRJZyXrXA/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/NpRJZyXrXA/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/NpRJZyXrXA/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/NpRJZyXrXA/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/NpRJZyXrXA/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/NpRJZyXrXA/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/NpRJZyXrXA/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/NpRJZyXrXA/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.002.01.bed Z (BAM input).. ok
351: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok
352: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
353: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
354: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
355: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
356: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
357: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
358: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
359: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
360: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
361: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
362: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
363: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
364: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
365: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
366: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
367: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
368: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
369: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
370: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
371: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
372: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
373: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
374: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
375: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
376: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
377: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
378: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
379: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
380: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
381: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
382: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
383: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
384: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
385: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
386: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
387: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
388: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
389: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
390: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
391: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
392: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
393: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
394: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap (BAM input).. ok
395: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap (BAM input).. ok
396: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok
397: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok
398: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok
399: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok
400: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok
401: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok
402: Make BAM with no M5/UR tags .. ok
403: Add @SQ with -t (SAM -> SAM) .. ok
404: Add @SQ with -T (SAM -> SAM) .. ok
405: Add @SQ with -t (BAM -> SAM) .. ok
406: Add @SQ with -T (BAM -> SAM) .. ok
407: Add @SQ with -t (SAM -> BAM) .. ok
408: Add @SQ with -T (SAM -> BAM) .. ok
409: Add @SQ with -t (BAM -> BAM) .. ok
410: Add @SQ with -T (BAM -> BAM) .. ok
411: Add @SQ with -t (SAM -> CRAM) .. ok
412: Add @SQ with -T (SAM -> CRAM) .. ok
413: Add @SQ with -t (BAM -> CRAM) .. ok
414: Add @SQ with -T (BAM -> CRAM) .. ok
415: Make CRAM with no UR field .. ok
416: Decoding CRAM with no UR field via -T .. ok
417: CIGAR B-operator removal .. ok
418: Big SAM -> BAM .. ok
419: Big SAM -> BAM (2 threads) .. ok
420: Big SAM -> BAM (4 threads) .. ok
421: Big SAM -> CRAM .. ok
422: Big SAM -> CRAM (2 threads) .. ok
423: Big SAM -> CRAM (4 threads) .. ok
424: Subsample 0.2 (SAM input) ............ ok
425: Subsample 0.5 (SAM input) ............ ok
426: Subsample 0.8 (SAM input) ............ ok
427: Subsample 0.2 (BAM input) ............ ok
428: Subsample 0.5 (BAM input) ............ ok
429: Subsample 0.8 (BAM input) ............ ok
430: Subsample 0.2 (CRAM input) ............ ok
431: Subsample 0.5 (CRAM input) ............ ok
432: Subsample 0.8 (CRAM input) ............ ok
433: SAM add PG .. ok
434: Unset dup flag, remove dt and do tags .. ok
435: Unmap dup flagged reads. .. ok
436: Unmap dup flagged reads. .. ok
437: fetch pairs .. ok
438: fetch pairs .. ok
439: 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/NpRJZyXrXA/bam2fq.discard.s.fq -0 /tmp/NpRJZyXrXA/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/NpRJZyXrXA/bam2fq.discard.s.fq -0 /tmp/NpRJZyXrXA/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/eDPsI7N9v2 - /<<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/NpRJZyXrXA/merge.tag.1.bam /tmp/NpRJZyXrXA/merge.tag.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/NpRJZyXrXA/merge.tag.3.bam /tmp/NpRJZyXrXA/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/NpRJZyXrXA/merge.bed.1.bam /tmp/NpRJZyXrXA/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/YVnAIuLiD2 - /<<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/NpRJZyXrXA/merge.tag.1.bam /tmp/NpRJZyXrXA/merge.tag.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/NpRJZyXrXA/merge.tag.3.bam /tmp/NpRJZyXrXA/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/NpRJZyXrXA/merge.bed.1.bam /tmp/NpRJZyXrXA/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/NpRJZyXrXA/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/NpRJZyXrXA/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/NpRJZyXrXA/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/NpRJZyXrXA/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/NpRJZyXrXA/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/NpRJZyXrXA/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/NpRJZyXrXA/longref.sam.gz
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools view -h --no-PG /tmp/NpRJZyXrXA/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/NpRJZyXrXA/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/NpRJZyXrXA/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 .. 929
passed .. 885
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-DxZhiYFE
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-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-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-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-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/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/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
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
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 1702653431 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 722317 new size 744711
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
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bd
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bd/d66e3eaf12f7a41375ee36dae49f9167d905d9.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bd/d66e3eaf12f7a41375ee36dae49f9167d905d9.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/bd/d66e3eaf12f7a41375ee36dae49f9167d905d9.debug debian/samtools/usr/bin/samtools
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ab
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ab/89e04af761d544c160484546dfca280d39d3e3.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ab/89e04af761d544c160484546dfca280d39d3e3.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ab/89e04af761d544c160484546dfca280d39d3e3.debug debian/samtools/usr/bin/maq2sam-long
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/76
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/76/37c31ae41deb79e720dcf2654ef806f8764bbf.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/76/37c31ae41deb79e720dcf2654ef806f8764bbf.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/76/37c31ae41deb79e720dcf2654ef806f8764bbf.debug debian/samtools/usr/bin/ace2sam
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ee
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ee/166bf44c1ea1adc41aa1eb654029a9d203cd57.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ee/166bf44c1ea1adc41aa1eb654029a9d203cd57.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ee/166bf44c1ea1adc41aa1eb654029a9d203cd57.debug debian/samtools/usr/bin/maq2sam-short
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65/6ee279ffaeac968195f1516c5b9f896d2e8b66.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65/6ee279ffaeac968195f1516c5b9f896d2e8b66.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65/6ee279ffaeac968195f1516c5b9f896d2e8b66.debug debian/samtools/usr/bin/md5fa
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fd
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fd/77a25dd64bbc615d73d1e94727cb84e78571c5.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fd/77a25dd64bbc615d73d1e94727cb84e78571c5.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fd/77a25dd64bbc615d73d1e94727cb84e78571c5.debug debian/samtools/usr/bin/md5sum-lite
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/aa
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/aa/fd9903d3194e4504df0f71e9ef54313ec4d5e0.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/aa/fd9903d3194e4504df0f71e9ef54313ec4d5e0.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/aa/fd9903d3194e4504df0f71e9ef54313ec4d5e0.debug debian/samtools/usr/bin/wgsim
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/samtools debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
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=656ee279ffaeac968195f1516c5b9f896d2e8b66 7637c31ae41deb79e720dcf2654ef806f8764bbf aafd9903d3194e4504df0f71e9ef54313ec4d5e0 ab89e04af761d544c160484546dfca280d39d3e3 bdd66e3eaf12f7a41375ee36dae49f9167d905d9 ee166bf44c1ea1adc41aa1eb654029a9d203cd57 fd77a25dd64bbc615d73d1e94727cb84e78571c5" -DSection=debug -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 ${perl:Depends} unused, but is defined
chmod 0644 -- debian/samtools/DEBIAN/control
dh_md5sums -a
install -m0755 -d debian/samtools/DEBIAN
cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/samtools/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --root-owner-group --build debian/samtools ..
dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root ..
dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.19-1_armhf.deb'.
dpkg-deb: building package 'samtools' in '../samtools_1.19-1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../samtools_1.19-1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../samtools_1.19-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-source: info: using options from samtools-1.19/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-12-18T06:26:38Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
samtools_1.19-1_armhf.changes:
------------------------------
Format: 1.8
Date: Fri, 15 Dec 2023 16:17:11 +0100
Source: samtools
Binary: samtools samtools-dbgsym
Architecture: armhf
Version: 1.19-1
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
samtools - processing sequence alignments in SAM, BAM and CRAM formats
Changes:
samtools (1.19-1) unstable; urgency=medium
.
* [73082b5] New upstream version 1.19
* [b86781d] d/rules: adjust dh_instalchangelogs.
Upstream NEWS file has been renamed NEWS.md.
Checksums-Sha1:
ccaf0ffb783c21a0be75d1c391bf2c7aa999b541 930476 samtools-dbgsym_1.19-1_armhf.deb
566b334a8ad98d0ba5099c5e28420bc9b222d67e 6109 samtools_1.19-1_armhf.buildinfo
aa9a20c8cd488b49773fd024f9dedc7fb946aa39 593400 samtools_1.19-1_armhf.deb
Checksums-Sha256:
4117ee83cee9b3d5143fb6f6e6faec85df876f11e354c2e143f38c4efe5de5c1 930476 samtools-dbgsym_1.19-1_armhf.deb
6f5d2129f1f5a12e24bbd81e89ddc37ac5fda464c8ac33f30e4fd1030bdc36b0 6109 samtools_1.19-1_armhf.buildinfo
bb9e1e11a64936c0b6a54d9a038f1cdd0ce0334498e8030cf276591a3592010c 593400 samtools_1.19-1_armhf.deb
Files:
14f4bdd8ac269bdba16868c626592724 930476 debug optional samtools-dbgsym_1.19-1_armhf.deb
bb1ec7ab3335ba94ecea6ab67685dccc 6109 science optional samtools_1.19-1_armhf.buildinfo
4bb2ea90952b5493f7c6734f45ed8fe4 593400 science optional samtools_1.19-1_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: samtools
Binary: samtools samtools-dbgsym
Architecture: armhf
Version: 1.19-1
Checksums-Md5:
14f4bdd8ac269bdba16868c626592724 930476 samtools-dbgsym_1.19-1_armhf.deb
4bb2ea90952b5493f7c6734f45ed8fe4 593400 samtools_1.19-1_armhf.deb
Checksums-Sha1:
ccaf0ffb783c21a0be75d1c391bf2c7aa999b541 930476 samtools-dbgsym_1.19-1_armhf.deb
aa9a20c8cd488b49773fd024f9dedc7fb946aa39 593400 samtools_1.19-1_armhf.deb
Checksums-Sha256:
4117ee83cee9b3d5143fb6f6e6faec85df876f11e354c2e143f38c4efe5de5c1 930476 samtools-dbgsym_1.19-1_armhf.deb
bb9e1e11a64936c0b6a54d9a038f1cdd0ce0334498e8030cf276591a3592010c 593400 samtools_1.19-1_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Mon, 18 Dec 2023 06:26:38 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.71-3),
autoconf-archive (= 20220903-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-14),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
base-passwd (= 3.6.2),
bash (= 5.2.15-2),
bash-completion (= 1:2.11-8),
binutils (= 2.41-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
binutils-common (= 2.41-6+rpi1),
bsdextrautils (= 2.39.3-2),
bsdutils (= 1:2.39.3-2),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
coreutils (= 9.1-1),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-10+rpi1),
cpp-13 (= 13.2.0-5+rpi1),
dash (= 0.5.12-6),
debconf (= 1.5.82),
debhelper (= 13.11.8),
debianutils (= 5.14),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.10-1),
dpkg (= 1.22.1+rpi1),
dpkg-dev (= 1.22.1+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-5+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-10+rpi1),
gcc-12-base (= 12.3.0-10+rpi1),
gcc-13 (= 13.2.0-5+rpi1),
gcc-13-base (= 13.2.0-5+rpi1),
gettext (= 0.21-14),
gettext-base (= 0.21-14),
grep (= 3.11-3),
groff-base (= 1.23.0-3),
gzip (= 1.12-1),
hostname (= 3.23+nmu1),
init-system-helpers (= 1.65.2),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-3),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 13.2.0-5+rpi1),
libatomic1 (= 13.2.0-5+rpi1),
libattr1 (= 1:2.5.1-4),
libaudit-common (= 1:3.1.1-1),
libaudit1 (= 1:3.1.1-1),
libbinutils (= 2.41-6+rpi1),
libblkid1 (= 2.39.3-2),
libbrotli1 (= 1.1.0-2),
libbz2-1.0 (= 1.0.8-5+b2),
libbz2-dev (= 1.0.8-5+b2),
libc-bin (= 2.37-12+rpi2),
libc-dev-bin (= 2.37-12+rpi2),
libc6 (= 2.37-12+rpi2),
libc6-dev (= 2.37-12+rpi2),
libcap-ng0 (= 0.8.3-1+b1),
libcap2 (= 1:2.66-4),
libcc1-0 (= 13.2.0-5+rpi1),
libcom-err2 (= 1.47.0-2),
libcrypt-dev (= 1:4.4.36-2),
libcrypt1 (= 1:4.4.36-2),
libctf-nobfd0 (= 2.41-6+rpi1),
libctf0 (= 2.41-6+rpi1),
libcurl3-gnutls (= 8.4.0-2+rpi1),
libcurl4-gnutls-dev (= 8.4.0-2+rpi1),
libdb5.3 (= 5.3.28+dfsg2-2),
libdebconfclient0 (= 0.271),
libdebhelper-perl (= 13.11.8),
libdeflate-dev (= 1.18-1),
libdeflate0 (= 1.18-1),
libdpkg-perl (= 1.22.1+rpi1),
libelf1 (= 0.188-2.1+rpi1),
libffi8 (= 3.4.4-1),
libfile-stripnondeterminism-perl (= 1.13.1-1),
libgcc-12-dev (= 12.3.0-10+rpi1),
libgcc-13-dev (= 13.2.0-5+rpi1),
libgcc-s1 (= 13.2.0-5+rpi1),
libgcrypt20 (= 1.10.2-3),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libgmp10 (= 2:6.3.0+dfsg-2),
libgnutls30 (= 3.8.1-4),
libgomp1 (= 13.2.0-5+rpi1),
libgpg-error0 (= 1.47-2),
libgssapi-krb5-2 (= 1.20.1-4),
libhogweed6 (= 3.9.1-2),
libhts-dev (= 1.18+ds-1),
libhts3 (= 1.18+ds-1),
libhtscodecs2 (= 1.5.2-1),
libicu72 (= 72.1-4),
libidn2-0 (= 2.3.4-1),
libio-pty-perl (= 1:1.17-1),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libk5crypto3 (= 1.20.1-4),
libkeyutils1 (= 1.6.3-2),
libkrb5-3 (= 1.20.1-4),
libkrb5support0 (= 1.20.1-4),
libldap-2.5-0 (= 2.5.13+dfsg-5+rpi1),
liblz4-1 (= 1.9.4-1+rpi1+b1),
liblzma-dev (= 5.4.5-0.1),
liblzma5 (= 5.4.5-0.1),
libmagic-mgc (= 1:5.45-2),
libmagic1 (= 1:5.45-2),
libmd0 (= 1.1.0-1),
libmount1 (= 2.39.3-2),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libncurses-dev (= 6.4+20231209-1),
libncurses6 (= 6.4+20231209-1),
libncursesw6 (= 6.4+20231209-1),
libnettle8 (= 3.9.1-2),
libnghttp2-14 (= 1.58.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libp11-kit0 (= 0.25.0-5),
libpam-modules (= 1.5.2-9.1),
libpam-modules-bin (= 1.5.2-9.1),
libpam-runtime (= 1.5.2-9.1),
libpam0g (= 1.5.2-9.1),
libpcre2-8-0 (= 10.42-4),
libperl5.36 (= 5.36.0-9),
libpipeline1 (= 1.5.7-1),
libpkgconf3 (= 1.8.1-1),
libpsl5 (= 0.21.2-1+b1),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.28+dfsg1-3),
libsasl2-modules-db (= 2.1.28+dfsg1-3),
libseccomp2 (= 2.5.4-1+rpi1+b1),
libselinux1 (= 3.5-1),
libsframe1 (= 2.41-6+rpi1),
libsmartcols1 (= 2.39.3-2),
libssh2-1 (= 1.11.0-3),
libssl3 (= 3.0.11-1),
libstdc++-13-dev (= 13.2.0-5+rpi1),
libstdc++6 (= 13.2.0-5+rpi1),
libsub-override-perl (= 0.10-1),
libsystemd0 (= 254.5-1+rpi1),
libtasn1-6 (= 4.19.0-3),
libtinfo6 (= 6.4+20231209-1),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtool (= 2.4.7-7),
libubsan1 (= 13.2.0-5+rpi1),
libuchardet0 (= 0.0.8-1),
libudev1 (= 254.5-1+rpi1),
libunistring5 (= 1.1-2),
libuuid1 (= 2.39.3-2),
libxml2 (= 2.9.14+dfsg-1.3),
libzstd1 (= 1.5.5+dfsg2-2),
linux-libc-dev (= 6.5.6-1+rpi1),
login (= 1:4.13+dfsg1-3),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.12.0-1),
mawk (= 1.3.4.20230808-1),
ncurses-base (= 6.4+20231209-1),
ncurses-bin (= 6.4+20231209-1),
patch (= 2.7.6-7),
perl (= 5.36.0-9),
perl-base (= 5.36.0-9),
perl-modules-5.36 (= 5.36.0-9),
pkg-config (= 1.8.1-1),
pkgconf (= 1.8.1-1),
pkgconf-bin (= 1.8.1-1),
po-debconf (= 1.0.21+nmu1),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-1),
sensible-utils (= 0.0.20),
sysvinit-utils (= 3.08-3),
tabix (= 1.18+ds-1),
tar (= 1.34+dfsg-1.2),
usr-is-merged (= 37),
util-linux (= 2.39.3-2),
xz-utils (= 5.4.5-0.1),
zlib1g (= 1:1.2.13.dfsg-3),
zlib1g-dev (= 1:1.2.13.dfsg-3)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1702653431"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
samtools-dbgsym_1.19-1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 930476 bytes: control archive=900 bytes.
619 bytes, 12 lines control
830 bytes, 8 lines md5sums
Package: samtools-dbgsym
Source: samtools
Version: 1.19-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1006
Depends: samtools (= 1.19-1)
Section: debug
Priority: optional
Description: debug symbols for samtools
Build-Ids: 656ee279ffaeac968195f1516c5b9f896d2e8b66 7637c31ae41deb79e720dcf2654ef806f8764bbf aafd9903d3194e4504df0f71e9ef54313ec4d5e0 ab89e04af761d544c160484546dfca280d39d3e3 bdd66e3eaf12f7a41375ee36dae49f9167d905d9 ee166bf44c1ea1adc41aa1eb654029a9d203cd57 fd77a25dd64bbc615d73d1e94727cb84e78571c5
drwxr-xr-x root/root 0 2023-12-15 15:17 ./
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/lib/
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/lib/debug/
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/lib/debug/.build-id/65/
-rw-r--r-- root/root 10524 2023-12-15 15:17 ./usr/lib/debug/.build-id/65/6ee279ffaeac968195f1516c5b9f896d2e8b66.debug
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/lib/debug/.build-id/76/
-rw-r--r-- root/root 24688 2023-12-15 15:17 ./usr/lib/debug/.build-id/76/37c31ae41deb79e720dcf2654ef806f8764bbf.debug
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/lib/debug/.build-id/aa/
-rw-r--r-- root/root 22200 2023-12-15 15:17 ./usr/lib/debug/.build-id/aa/fd9903d3194e4504df0f71e9ef54313ec4d5e0.debug
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/lib/debug/.build-id/ab/
-rw-r--r-- root/root 10784 2023-12-15 15:17 ./usr/lib/debug/.build-id/ab/89e04af761d544c160484546dfca280d39d3e3.debug
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/lib/debug/.build-id/bd/
-rw-r--r-- root/root 916832 2023-12-15 15:17 ./usr/lib/debug/.build-id/bd/d66e3eaf12f7a41375ee36dae49f9167d905d9.debug
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/lib/debug/.build-id/ee/
-rw-r--r-- root/root 10780 2023-12-15 15:17 ./usr/lib/debug/.build-id/ee/166bf44c1ea1adc41aa1eb654029a9d203cd57.debug
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/lib/debug/.build-id/fd/
-rw-r--r-- root/root 7256 2023-12-15 15:17 ./usr/lib/debug/.build-id/fd/77a25dd64bbc615d73d1e94727cb84e78571c5.debug
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 3604 2023-12-15 15:17 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/share/
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/share/doc/
lrwxrwxrwx root/root 0 2023-12-15 15:17 ./usr/share/doc/samtools-dbgsym -> samtools
samtools_1.19-1_armhf.deb
-------------------------
new Debian package, version 2.0.
size 593400 bytes: control archive=2940 bytes.
834 bytes, 17 lines control
5675 bytes, 83 lines md5sums
Package: samtools
Version: 1.19-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1257
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.
drwxr-xr-x root/root 0 2023-12-15 15:17 ./
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/bin/
-rwxr-xr-x root/root 18012 2023-12-15 15:17 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5443 2023-12-15 15:17 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3360 2023-12-15 15:17 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 17996 2023-12-15 15:17 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 3300 2023-12-15 15:17 ./usr/bin/fasta-sanitize.pl
-rwxr-xr-x root/root 6121 2023-12-15 15:17 ./usr/bin/interpolate_sam.pl
-rwxr-xr-x root/root 9820 2023-12-15 15:17 ./usr/bin/maq2sam-long
-rwxr-xr-x root/root 9820 2023-12-15 15:17 ./usr/bin/maq2sam-short
-rwxr-xr-x root/root 9820 2023-12-15 15:17 ./usr/bin/md5fa
-rwxr-xr-x root/root 5724 2023-12-15 15:17 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 7969 2023-12-15 15:17 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 44331 2023-12-15 15:17 ./usr/bin/plot-ampliconstats
-rwxr-xr-x root/root 55292 2023-12-15 15:17 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3204 2023-12-15 15:17 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8957 2023-12-15 15:17 ./usr/bin/sam2vcf.pl
-rwxr-xr-x root/root 647800 2023-12-15 15:17 ./usr/bin/samtools
-rwxr-xr-x root/root 16474 2023-12-15 15:17 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11333 2023-12-15 15:17 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3905 2023-12-15 15:17 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 18052 2023-12-15 15:17 ./usr/bin/wgsim
-rwxr-xr-x root/root 12542 2023-12-15 15:17 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3579 2023-12-15 15:17 ./usr/bin/zoom2sam.pl
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/share/
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/share/commonwl/
-rwxr-xr-x root/root 1906 2023-12-15 15:06 ./usr/share/commonwl/samtools-faidx.cwl
-rwxr-xr-x root/root 1979 2023-12-15 15:06 ./usr/share/commonwl/samtools-index.cwl
-rwxr-xr-x root/root 1627 2023-12-15 15:06 ./usr/share/commonwl/samtools-rmdup.cwl
-rwxr-xr-x root/root 2834 2023-12-15 15:06 ./usr/share/commonwl/samtools-sort.cwl
-rwxr-xr-x root/root 6224 2023-12-15 15:06 ./usr/share/commonwl/samtools-view.cwl
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2023-12-12 14:02 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 497 2023-12-15 15:06 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 2479 2023-12-12 14:02 ./usr/share/doc/samtools/README.gz
-rw-r--r-- root/root 313 2023-12-15 15:06 ./usr/share/doc/samtools/README.test
-rw-r--r-- root/root 1917 2023-12-15 15:17 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 35148 2023-12-12 14:02 ./usr/share/doc/samtools/changelog.gz
-rw-r--r-- root/root 2250 2023-12-15 15:07 ./usr/share/doc/samtools/copyright
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 1315 2023-12-12 14:02 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 3225 2023-12-12 14:02 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2023-12-15 15:17 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 98 2023-12-12 14:02 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2023-12-12 14:02 ./usr/share/doc/samtools/examples/toy.sam
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/share/lintian/
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 168 2023-12-15 15:06 ./usr/share/lintian/overrides/samtools
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/share/man/
drwxr-xr-x root/root 0 2023-12-15 15:17 ./usr/share/man/man1/
-rw-r--r-- root/root 462 2023-12-15 15:17 ./usr/share/man/man1/ace2sam.1.gz
-rw-r--r-- root/root 1639 2023-12-15 15:17 ./usr/share/man/man1/samtools-addreplacerg.1.gz
-rw-r--r-- root/root 2355 2023-12-15 15:17 ./usr/share/man/man1/samtools-ampliconclip.1.gz
-rw-r--r-- root/root 5837 2023-12-15 15:17 ./usr/share/man/man1/samtools-ampliconstats.1.gz
-rw-r--r-- root/root 2016 2023-12-15 15:17 ./usr/share/man/man1/samtools-bedcov.1.gz
-rw-r--r-- root/root 2301 2023-12-15 15:17 ./usr/share/man/man1/samtools-calmd.1.gz
-rw-r--r-- root/root 1541 2023-12-15 15:17 ./usr/share/man/man1/samtools-cat.1.gz
-rw-r--r-- root/root 2475 2023-12-15 15:17 ./usr/share/man/man1/samtools-collate.1.gz
-rw-r--r-- root/root 6075 2023-12-15 15:17 ./usr/share/man/man1/samtools-consensus.1.gz
-rw-r--r-- root/root 2685 2023-12-15 15:17 ./usr/share/man/man1/samtools-coverage.1.gz
-rw-r--r-- root/root 3177 2023-12-15 15:17 ./usr/share/man/man1/samtools-cram-size.1.gz
-rw-r--r-- root/root 1753 2023-12-15 15:17 ./usr/share/man/man1/samtools-depad.1.gz
-rw-r--r-- root/root 3189 2023-12-15 15:17 ./usr/share/man/man1/samtools-depth.1.gz
-rw-r--r-- root/root 1685 2023-12-15 15:17 ./usr/share/man/man1/samtools-dict.1.gz
-rw-r--r-- root/root 2117 2023-12-15 15:17 ./usr/share/man/man1/samtools-faidx.1.gz
-rw-r--r-- root/root 4251 2023-12-15 15:17 ./usr/share/man/man1/samtools-fasta.1.gz
lrwxrwxrwx root/root 0 2023-12-15 15:17 ./usr/share/man/man1/samtools-fastq.1.gz -> samtools-fasta.1.gz
-rw-r--r-- root/root 1652 2023-12-15 15:17 ./usr/share/man/man1/samtools-fixmate.1.gz
-rw-r--r-- root/root 1498 2023-12-15 15:17 ./usr/share/man/man1/samtools-flags.1.gz
-rw-r--r-- root/root 2601 2023-12-15 15:17 ./usr/share/man/man1/samtools-flagstat.1.gz
-rw-r--r-- root/root 2167 2023-12-15 15:17 ./usr/share/man/man1/samtools-fqidx.1.gz
-rw-r--r-- root/root 1334 2023-12-15 15:17 ./usr/share/man/man1/samtools-head.1.gz
-rw-r--r-- root/root 1414 2023-12-15 15:17 ./usr/share/man/man1/samtools-idxstats.1.gz
-rw-r--r-- root/root 3576 2023-12-15 15:17 ./usr/share/man/man1/samtools-import.1.gz
-rw-r--r-- root/root 1950 2023-12-15 15:17 ./usr/share/man/man1/samtools-index.1.gz
-rw-r--r-- root/root 3903 2023-12-15 15:17 ./usr/share/man/man1/samtools-markdup.1.gz
-rw-r--r-- root/root 3688 2023-12-15 15:17 ./usr/share/man/man1/samtools-merge.1.gz
-rw-r--r-- root/root 7504 2023-12-15 15:17 ./usr/share/man/man1/samtools-mpileup.1.gz
-rw-r--r-- root/root 1439 2023-12-15 15:17 ./usr/share/man/man1/samtools-phase.1.gz
-rw-r--r-- root/root 1678 2023-12-15 15:17 ./usr/share/man/man1/samtools-quickcheck.1.gz
-rw-r--r-- root/root 1879 2023-12-15 15:17 ./usr/share/man/man1/samtools-reference.1.gz
-rw-r--r-- root/root 1962 2023-12-15 15:17 ./usr/share/man/man1/samtools-reheader.1.gz
-rw-r--r-- root/root 2306 2023-12-15 15:17 ./usr/share/man/man1/samtools-reset.1.gz
-rw-r--r-- root/root 1470 2023-12-15 15:17 ./usr/share/man/man1/samtools-rmdup.1.gz
-rw-r--r-- root/root 2281 2023-12-15 15:17 ./usr/share/man/man1/samtools-samples.1.gz
-rw-r--r-- root/root 4722 2023-12-15 15:17 ./usr/share/man/man1/samtools-sort.1.gz
-rw-r--r-- root/root 2577 2023-12-15 15:17 ./usr/share/man/man1/samtools-split.1.gz
-rw-r--r-- root/root 6259 2023-12-15 15:17 ./usr/share/man/man1/samtools-stats.1.gz
-rw-r--r-- root/root 1427 2023-12-15 15:17 ./usr/share/man/man1/samtools-targetcut.1.gz
-rw-r--r-- root/root 2046 2023-12-15 15:17 ./usr/share/man/man1/samtools-tview.1.gz
-rw-r--r-- root/root 7191 2023-12-15 15:17 ./usr/share/man/man1/samtools-view.1.gz
-rw-r--r-- root/root 15957 2023-12-15 15:17 ./usr/share/man/man1/samtools.1.gz
-rw-r--r-- root/root 410 2023-12-15 15:17 ./usr/share/man/man1/samtools.pl.1.gz
-rw-r--r-- root/root 518 2023-12-15 15:17 ./usr/share/man/man1/wgsim.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 30200
Build-Time: 70
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 28
Job: samtools_1.19-1
Machine Architecture: arm64
Package: samtools
Package-Time: 108
Source-Version: 1.19-1
Space: 30200
Status: successful
Version: 1.19-1
--------------------------------------------------------------------------------
Finished at 2023-12-18T06:26:38Z
Build needed 00:01:48, 30200k disk space