samtools →
1.13-4 →
armhf → 2021-10-28 07:01:30
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| samtools 1.13-4 (armhf) Thu, 28 Oct 2021 06:53:02 +0000 |
+==============================================================================+
Package: samtools
Version: 1.13-4
Source Version: 1.13-4
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-12d56bd9-afd8-450e-b5de-e10fd933c6fe' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.9 MB in 12s (2210 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 4574 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main samtools 1.13-4 (dsc) [2294 B]
Get:2 http://172.17.0.1/private bookworm-staging/main samtools 1.13-4 (tar) [4550 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main samtools 1.13-4 (diff) [21.6 kB]
Fetched 4574 kB in 1s (4434 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/samtools-m4gpuz/samtools-1.13' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/samtools-m4gpuz' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-gOBRZQ/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-gOBRZQ/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (10.2 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (66.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12501 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.13~), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0), liblzma-dev, libbz2-dev
Filtered Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.13~), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0), liblzma-dev, libbz2-dev
dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-samtools-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive ./ Sources [598 B]
Get:5 copy:/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive ./ Packages [670 B]
Fetched 2601 B in 0s (12.5 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install samtools build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional 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
libglib2.0-0 libhts-dev libhts3 libhtscodecs2 libicu67 libio-pty-perl
liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses5-dev
libncurses6 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsigsegv2
libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
pkg-config po-debconf sensible-utils tabix zlib1g-dev
Suggested packages:
gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev
libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev
libldap2-dev librtmp-dev libssh2-1-dev liblzma-doc ncurses-doc libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl
libglib2.0-data shared-mime-info xdg-user-dirs libgpm2 publicsuffix
libltdl-dev 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
libglib2.0-0 libhts-dev libhts3 libhtscodecs2 libicu67 libio-pty-perl
liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses5-dev
libncurses6 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsigsegv2
libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
pkg-config po-debconf sbuild-build-depends-samtools-dummy sensible-utils
tabix zlib1g-dev
0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded.
Need to get 26.7 MB of archives.
After this operation, 90.2 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-gOBRZQ/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [956 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf autoconf-archive all 20210219-2 [767 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf bash-completion all 1:2.11-4 [234 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.5-1 [823 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-2 [15.5 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.3 [301 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3 [375 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libdeflate0 armhf 1.8-1 [44.1 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.8-1 [40.4 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.0-1 [1208 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.1.1-3 [49.8 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2 [339 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2 [219 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf libhts-dev armhf 1.13+ds-2 [4049 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf libio-pty-perl armhf 1:1.15-2 [36.1 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf libncurses-dev armhf 6.2+20201114-4 [288 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libncurses5-dev armhf 6.2+20201114-4 [940 B]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf tabix armhf 1.13+ds-2 [292 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../38-libssh2-1_1.10.0-2_armhf.deb ...
Unpacking libssh2-1:armhf (1.10.0-2) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../39-libcurl3-gnutls_7.74.0-1.3_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.74.0-1.3) ...
Selecting previously unselected package libcurl4-gnutls-dev:armhf.
Preparing to unpack .../40-libcurl4-gnutls-dev_7.74.0-1.3_armhf.deb ...
Unpacking libcurl4-gnutls-dev:armhf (7.74.0-1.3) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../41-libdeflate0_1.8-1_armhf.deb ...
Unpacking libdeflate0:armhf (1.8-1) ...
Selecting previously unselected package libdeflate-dev:armhf.
Preparing to unpack .../42-libdeflate-dev_1.8-1_armhf.deb ...
Unpacking libdeflate-dev:armhf (1.8-1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../43-libglib2.0-0_2.70.0-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.70.0-1) ...
Selecting previously unselected package libhtscodecs2:armhf.
Preparing to unpack .../44-libhtscodecs2_1.1.1-3_armhf.deb ...
Unpacking libhtscodecs2:armhf (1.1.1-3) ...
Selecting previously unselected package libhts3:armhf.
Preparing to unpack .../45-libhts3_1.13+ds-2_armhf.deb ...
Unpacking libhts3:armhf (1.13+ds-2) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../46-liblzma-dev_5.2.5-2_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.5-2) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../47-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package libhts-dev:armhf.
Preparing to unpack .../48-libhts-dev_1.13+ds-2_armhf.deb ...
Unpacking libhts-dev:armhf (1.13+ds-2) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../49-libio-pty-perl_1%3a1.15-2_armhf.deb ...
Unpacking libio-pty-perl (1:1.15-2) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../50-libncurses6_6.2+20201114-4_armhf.deb ...
Unpacking libncurses6:armhf (6.2+20201114-4) ...
Selecting previously unselected package libncurses-dev:armhf.
Preparing to unpack .../51-libncurses-dev_6.2+20201114-4_armhf.deb ...
Unpacking libncurses-dev:armhf (6.2+20201114-4) ...
Selecting previously unselected package libncurses5-dev:armhf.
Preparing to unpack .../52-libncurses5-dev_6.2+20201114-4_armhf.deb ...
Unpacking libncurses5-dev:armhf (6.2+20201114-4) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../53-pkg-config_0.29.2-1_armhf.deb ...
Unpacking pkg-config (0.29.2-1) ...
Selecting previously unselected package tabix.
Preparing to unpack .../54-tabix_1.13+ds-2_armhf.deb ...
Unpacking tabix (1.13+ds-2) ...
Selecting previously unselected package sbuild-build-depends-samtools-dummy.
Preparing to unpack .../55-sbuild-build-depends-samtools-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
Setting up libhtscodecs2:armhf (1.1.1-3) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.37.2-4) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libio-pty-perl (1:1.15-2) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.70.0-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.5.2) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libdeflate0:armhf (1.8-1) ...
Setting up gettext-base (0.21-4) ...
Setting up autoconf-archive (20210219-2) ...
Setting up file (1:5.39-3) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up bash-completion (1:2.11-4) ...
Setting up libncurses6:armhf (6.2+20201114-4) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
Setting up pkg-config (0.29.2-1) ...
Setting up liblzma-dev:armhf (5.2.5-2) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.10.0-2) ...
Setting up libdeflate-dev:armhf (1.8-1) ...
Setting up tabix (1.13+ds-2) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libbz2-dev:armhf (1.0.8-4) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-2) ...
Setting up libncurses-dev:armhf (6.2+20201114-4) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1.3) ...
Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.3) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-2) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up libncurses5-dev:armhf (6.2+20201114-4) ...
Setting up automake (1:1.16.5-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.13+ds-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.13+ds-2) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.5.2) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-11+rpi1 gcc-10_10.3.0-11+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-9+rpi1 linux-libc-dev_5.14.9-2+rpi1
Package versions: adduser_3.118 apt_2.3.11 autoconf_2.71-2 autoconf-archive_20210219-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-3 bash-completion_1:2.11-4 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-11+rpi1 dash_0.5.11+git20210120+802ebd4-2 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-11+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-11+rpi1 gcc-10-base_10.3.0-11+rpi1 gcc-11-base_11.2.0-9+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_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.11 libarchive-zip-perl_1.68-1 libasan6_11.2.0-9+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-9+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-4 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-9+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcurl3-gnutls_7.74.0-1.3 libcurl4-gnutls-dev_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdeflate-dev_1.8-1 libdeflate0_1.8-1 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.0-2 libgcc-10-dev_10.3.0-11+rpi1 libgcc-s1_11.2.0-9+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libglib2.0-0_2.70.0-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-9+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libicu67_67.1-7 libidn2-0_2.3.2-2 libio-pty-perl_1:1.15-2 libisl23_0.24-2 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpfr6_4.1.0-3 libncurses-dev_6.2+20201114-4 libncurses5-dev_6.2+20201114-4 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libreadline8_8.1-2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.2-2+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-9+rpi1 libsub-override-perl_0.09-2 libsystemd0_249.5-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-9+rpi1 libuchardet0_0.0.7-1 libudev1_249.5-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.9-2+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-4 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tabix_1.13+ds-2 tar_1.34+dfsg-1 tzdata_2021d-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.7sNCAsOz/trustedkeys.kbx': General error
gpgv: Signature made Mon Oct 25 18:59:44 2021 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./samtools_1.13-4.dsc
dpkg-source: info: extracting samtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking samtools_1.13.orig.tar.gz
dpkg-source: info: unpacking samtools_1.13-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying reproducible.patch
dpkg-source: info: applying fix-ftbfs-mvprintw.patch
dpkg-source: info: applying samtools-fasta-q-whatis.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
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-12d56bd9-afd8-450e-b5de-e10fd933c6fe
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package samtools
dpkg-buildpackage: info: source version 1.13-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from samtools-1.13/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 --
install -d /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home
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
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*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o
rm -f samtools libbam.a 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
install -d /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home
./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 -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 -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 -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 -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -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
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 -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 -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 -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 -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 -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 -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 -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 -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 -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 "1.13"' > 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 -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 -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 -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.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 -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 -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.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 -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 -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 -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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -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
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -csru libbam.a bam_aux.o bam.o sam.o bam_plbuf.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.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_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.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 bam2bcf_indel.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 ./lz4/lz4.o libbam.a 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 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:-}
/usr/bin/bgzip -c -b 65272 -s 5 /tmp/CGFKdSjwrP/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 979200 -s 6 /tmp/CGFKdSjwrP/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 652804 -s 6 /tmp/CGFKdSjwrP/bgzip.dat.gz
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/CGFKdSjwrP/faidx.fa 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/CGFKdSjwrP/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/CGFKdSjwrP/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/CGFKdSjwrP/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/CGFKdSjwrP/faidx.fa 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/CGFKdSjwrP/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/CGFKdSjwrP/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/CGFKdSjwrP/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/CGFKdSjwrP/fqidx.fq 3:11-13
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/CGFKdSjwrP/fqidx.fq.gz 3:11-13
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/CGFKdSjwrP/fqidx.fq 2:998-1003
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/CGFKdSjwrP/fqidx.fq.gz 2:998-1003
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/CGFKdSjwrP/fqidx.fq 1:100-104
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/CGFKdSjwrP/fqidx.fq.gz 1:100-104
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/CGFKdSjwrP/fqidx.fq 1:99998-100007
.. ok
.. ok
/<<PKGBUILDDIR>>/samtools fqidx /tmp/CGFKdSjwrP/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/CGFKdSjwrP/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_index:
/<<PKGBUILDDIR>>/samtools view /tmp/CGFKdSjwrP/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view /tmp/CGFKdSjwrP/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/CGFKdSjwrP/test_input_1_b.bam.bai ref2
.. 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/CGFKdSjwrP/test_input_1_b.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam /tmp/CGFKdSjwrP/auto_indexed.csi && cat /tmp/CGFKdSjwrP/auto_indexed.csi
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.cram /tmp/CGFKdSjwrP/auto_indexed.crai && cat /tmp/CGFKdSjwrP/auto_indexed.crai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.sam /tmp/CGFKdSjwrP/auto_indexed.csi && cat /tmp/CGFKdSjwrP/auto_indexed.csi
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/CGFKdSjwrP/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/CGFKdSjwrP/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/CGFKdSjwrP/test_input_1_b.bam.bai ref2
.. 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/CGFKdSjwrP/test_input_1_b.bam.bai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.bam /tmp/CGFKdSjwrP/auto_indexed.csi && cat /tmp/CGFKdSjwrP/auto_indexed.csi
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.cram /tmp/CGFKdSjwrP/auto_indexed.crai && cat /tmp/CGFKdSjwrP/auto_indexed.crai
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 -c /<<PKGBUILDDIR>>/test/dat/auto_indexed.tmp.sam /tmp/CGFKdSjwrP/auto_indexed.csi && cat /tmp/CGFKdSjwrP/auto_indexed.csi
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/CGFKdSjwrP/mpileup.bam.list -f /tmp/CGFKdSjwrP/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/CGFKdSjwrP/mpileup.cram.list -f /tmp/CGFKdSjwrP/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/CGFKdSjwrP/mpileup.bam.urllist -f /tmp/CGFKdSjwrP/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/CGFKdSjwrP/mpileup.cram.urllist -f /tmp/CGFKdSjwrP/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uvDV -b /tmp/CGFKdSjwrP/mpileup.bam.list -f /tmp/CGFKdSjwrP/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uvDV -b /tmp/CGFKdSjwrP/mpileup.cram.list -f /tmp/CGFKdSjwrP/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/CGFKdSjwrP/mpileup.cram.list -f /tmp/CGFKdSjwrP/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/CGFKdSjwrP/mpileup.cram.list -f /tmp/CGFKdSjwrP/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/CGFKdSjwrP/mpileup.ref.fa.gz -r17:1050-1060 /tmp/CGFKdSjwrP/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/CGFKdSjwrP/mpileup.ref.fa.gz -r17:1050-1060 /tmp/CGFKdSjwrP/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, merge, mpileup, sort, split, quickcheck, fastq, fasta, import, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, tview, view, depad, 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
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools cat
Usage on stderr rather than stdout
.. expected failure
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 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 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_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/CGFKdSjwrP/view.001.fogn (SAM input) .. ok
50: Count -R /tmp/CGFKdSjwrP/view.001.fogn (SAM input) .. ok
51: Filter -R /tmp/CGFKdSjwrP/view.001.fogn (BAM input) .. ok
52: Count -R /tmp/CGFKdSjwrP/view.001.fogn (BAM input) .. ok
53: Filter -R /tmp/CGFKdSjwrP/view.001.fogn (CRAM input) .. ok
54: Count -R /tmp/CGFKdSjwrP/view.001.fogn (CRAM input) .. ok
55: Filter -R /tmp/CGFKdSjwrP/view.001.fogn -r grp2 (SAM input).. ok
56: Count -R /tmp/CGFKdSjwrP/view.001.fogn -r grp2 (SAM input).. ok
57: Filter -R /tmp/CGFKdSjwrP/view.001.fogn -r grp2 (BAM input).. ok
58: Count -R /tmp/CGFKdSjwrP/view.001.fogn -r grp2 (BAM input).. ok
59: Filter -R /tmp/CGFKdSjwrP/view.001.fogn -r grp2 (CRAM input).. ok
60: Count -R /tmp/CGFKdSjwrP/view.001.fogn -r grp2 (CRAM input).. ok
61: Filter -r grp2 -R /tmp/CGFKdSjwrP/view.001.fogn (SAM input).. ok
62: Count -r grp2 -R /tmp/CGFKdSjwrP/view.001.fogn (SAM input).. ok
63: Filter -r grp2 -R /tmp/CGFKdSjwrP/view.001.fogn (BAM input).. ok
64: Count -r grp2 -R /tmp/CGFKdSjwrP/view.001.fogn (BAM input).. ok
65: Filter -r grp2 -R /tmp/CGFKdSjwrP/view.001.fogn (CRAM input).. ok
66: Count -r grp2 -R /tmp/CGFKdSjwrP/view.001.fogn (CRAM input).. ok
67: Filter -N /tmp/CGFKdSjwrP/view.001.forn (SAM input) .. ok
68: Count -N /tmp/CGFKdSjwrP/view.001.forn (SAM input) .. ok
69: Filter -N /tmp/CGFKdSjwrP/view.001.forn (BAM input) .. ok
70: Count -N /tmp/CGFKdSjwrP/view.001.forn (BAM input) .. ok
71: Filter -N /tmp/CGFKdSjwrP/view.001.forn (CRAM input) .. ok
72: Count -N /tmp/CGFKdSjwrP/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/CGFKdSjwrP/view.001.fobc (SAM input) .. ok
86: Count -D BC:/tmp/CGFKdSjwrP/view.001.fobc (SAM input) .. ok
87: Filter -D BC:/tmp/CGFKdSjwrP/view.001.fobc (BAM input) .. ok
88: Count -D BC:/tmp/CGFKdSjwrP/view.001.fobc (BAM input) .. ok
89: Filter -D BC:/tmp/CGFKdSjwrP/view.001.fobc (CRAM input) .. ok
90: Count -D BC:/tmp/CGFKdSjwrP/view.001.fobc (CRAM input) .. ok
91: Filter -D BC:/tmp/CGFKdSjwrP/view.001.fobc -d BC:TGCA (SAM input).. ok
92: Count -D BC:/tmp/CGFKdSjwrP/view.001.fobc -d BC:TGCA (SAM input).. ok
93: Filter -D BC:/tmp/CGFKdSjwrP/view.001.fobc -d BC:TGCA (BAM input).. ok
94: Count -D BC:/tmp/CGFKdSjwrP/view.001.fobc -d BC:TGCA (BAM input).. ok
95: Filter -D BC:/tmp/CGFKdSjwrP/view.001.fobc -d BC:TGCA (CRAM input).. ok
96: Count -D BC:/tmp/CGFKdSjwrP/view.001.fobc -d BC:TGCA (CRAM input).. ok
97: Filter -d BC:TGCA -D BC:/tmp/CGFKdSjwrP/view.001.fobc (SAM input).. ok
98: Count -d BC:TGCA -D BC:/tmp/CGFKdSjwrP/view.001.fobc (SAM input).. ok
99: Filter -d BC:TGCA -D BC:/tmp/CGFKdSjwrP/view.001.fobc (BAM input).. ok
100: Count -d BC:TGCA -D BC:/tmp/CGFKdSjwrP/view.001.fobc (BAM input).. ok
101: Filter -d BC:TGCA -D BC:/tmp/CGFKdSjwrP/view.001.fobc (CRAM input).. ok
102: Count -d BC:TGCA -D BC:/tmp/CGFKdSjwrP/view.001.fobc (CRAM input).. ok
103: Filter -D RG:/tmp/CGFKdSjwrP/view.001.fogn (SAM input) .. ok
104: Count -D RG:/tmp/CGFKdSjwrP/view.001.fogn (SAM input) .. ok
105: Filter -D RG:/tmp/CGFKdSjwrP/view.001.fogn (BAM input) .. ok
106: Count -D RG:/tmp/CGFKdSjwrP/view.001.fogn (BAM input) .. ok
107: Filter -D RG:/tmp/CGFKdSjwrP/view.001.fogn (CRAM input).. ok
108: Count -D RG:/tmp/CGFKdSjwrP/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/CGFKdSjwrP/view.test115.sam -h -d TGCA /tmp/CGFKdSjwrP/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/CGFKdSjwrP/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/CGFKdSjwrP/view.test117.sam -h -d TGCA /tmp/CGFKdSjwrP/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/CGFKdSjwrP/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/CGFKdSjwrP/view.test119.sam -h -d TGCA /tmp/CGFKdSjwrP/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/CGFKdSjwrP/view.test006.cram --no-PG
.. expected failure
121: Filter -D BClong:/tmp/CGFKdSjwrP/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/CGFKdSjwrP/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/CGFKdSjwrP/view.test121.sam -h -D BClong:/tmp/CGFKdSjwrP/view.001.fobc /tmp/CGFKdSjwrP/view.001.sam --no-PG
.. expected failure
122: Count -D BClong:/tmp/CGFKdSjwrP/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/CGFKdSjwrP/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/CGFKdSjwrP/view.001.fobc /tmp/CGFKdSjwrP/view.001.sam --no-PG
.. expected failure
123: Filter -D BClong:/tmp/CGFKdSjwrP/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/CGFKdSjwrP/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/CGFKdSjwrP/view.test123.sam -h -D BClong:/tmp/CGFKdSjwrP/view.001.fobc /tmp/CGFKdSjwrP/view.test001.bam --no-PG
.. expected failure
124: Count -D BClong:/tmp/CGFKdSjwrP/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/CGFKdSjwrP/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/CGFKdSjwrP/view.001.fobc /tmp/CGFKdSjwrP/view.test001.bam --no-PG
.. expected failure
125: Filter -D BClong:/tmp/CGFKdSjwrP/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/CGFKdSjwrP/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -o /tmp/CGFKdSjwrP/view.test125.sam -h -D BClong:/tmp/CGFKdSjwrP/view.001.fobc /tmp/CGFKdSjwrP/view.test006.cram --no-PG
.. expected failure
126: Count -D BClong:/tmp/CGFKdSjwrP/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/CGFKdSjwrP/view.001.fobc"
Failed command:
/<<PKGBUILDDIR>>/samtools view -c -D BClong:/tmp/CGFKdSjwrP/view.001.fobc /tmp/CGFKdSjwrP/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/CGFKdSjwrP/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/CGFKdSjwrP/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/CGFKdSjwrP/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/CGFKdSjwrP/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/CGFKdSjwrP/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/CGFKdSjwrP/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/CGFKdSjwrP/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/CGFKdSjwrP/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/CGFKdSjwrP/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 -r grp2 (SAM input) .. ok
188: Count -x fa -r grp2 (SAM input) .. ok
189: Filter -x fa -r grp2 (BAM input) .. ok
190: Count -x fa -r grp2 (BAM input) .. ok
191: Filter -x fa -r grp2 (CRAM input) .. ok
192: Count -x fa -r grp2 (CRAM input) .. ok
193: Filter -x RG -r grp2 (SAM input) .. ok
194: Count -x RG -r grp2 (SAM input) .. ok
195: Filter -x RG -r grp2 (BAM input) .. ok
196: Count -x RG -r grp2 (BAM input) .. ok
197: Filter -x RG -r grp2 (CRAM input) .. ok
198: Count -x RG -r grp2 (CRAM input) .. ok
199: Filter -m 10 (SAM input) .. ok
200: Count -m 10 (SAM input) .. ok
201: Filter -m 10 (BAM input) .. ok
202: Count -m 10 (BAM input) .. ok
203: Filter -m 10 (CRAM input) .. ok
204: Count -m 10 (CRAM input) .. ok
205: Filter -m 11 (SAM input) .. ok
206: Count -m 11 (SAM input) .. ok
207: Filter -m 11 (BAM input) .. ok
208: Count -m 11 (BAM input) .. ok
209: Filter -m 11 (CRAM input) .. ok
210: Count -m 11 (CRAM input) .. ok
211: Filter -m 15 (SAM input) .. ok
212: Count -m 15 (SAM input) .. ok
213: Filter -m 15 (BAM input) .. ok
214: Count -m 15 (BAM input) .. ok
215: Filter -m 15 (CRAM input) .. ok
216: Count -m 15 (CRAM input) .. ok
217: Filter -m 16 (SAM input) .. ok
218: Count -m 16 (SAM input) .. ok
219: Filter -m 16 (BAM input) .. ok
220: Count -m 16 (BAM input) .. ok
221: Filter -m 16 (CRAM input) .. ok
222: Count -m 16 (CRAM input) .. ok
223: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok
224: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok
225: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok
226: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok
227: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok
228: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok
229: Filter -e [BC] (SAM input) .. ok
230: Count -e [BC] (SAM input) .. ok
231: Filter -e [BC] (BAM input) .. ok
232: Count -e [BC] (BAM input) .. ok
233: Filter -e [BC] (CRAM input) .. ok
234: Count -e [BC] (CRAM input) .. ok
235: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok
236: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok
237: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok
238: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok
239: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok
240: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok
241: Filter -e mapq >= 50 (SAM input) .. ok
242: Count -e mapq >= 50 (SAM input) .. ok
243: Filter -e mapq >= 50 (BAM input) .. ok
244: Count -e mapq >= 50 (BAM input) .. ok
245: Filter -e mapq >= 50 (CRAM input) .. ok
246: Count -e mapq >= 50 (CRAM input) .. ok
247: Filter -e mapq >= 99 (SAM input) .. ok
248: Count -e mapq >= 99 (SAM input) .. ok
249: Filter -e mapq >= 99 (BAM input) .. ok
250: Count -e mapq >= 99 (BAM input) .. ok
251: Filter -e mapq >= 99 (CRAM input) .. ok
252: Count -e mapq >= 99 (CRAM input) .. ok
253: Filter -e mapq >= 100 (SAM input) .. ok
254: Count -e mapq >= 100 (SAM input) .. ok
255: Filter -e mapq >= 100 (BAM input) .. ok
256: Count -e mapq >= 100 (BAM input) .. ok
257: Filter -e mapq >= 100 (CRAM input) .. ok
258: Count -e mapq >= 100 (CRAM input) .. ok
259: 1bp reads file SAM -> BAM -> SAM .. ok
260: 1bp reads file SAM -> CRAM -> SAM .. ok
260: Region Z (BAM input) .. ok
261: Count Z (BAM input) .. ok
262: Region Z (CRAM input) .. ok
263: Count Z (CRAM input) .. ok
264: Region Z:30 (BAM input) .. ok
265: Count Z:30 (BAM input) .. ok
266: Region Z:30 (CRAM input) .. ok
267: Count Z:30 (CRAM input) .. ok
268: Region Z:20-40 (BAM input) .. ok
269: Count Z:20-40 (BAM input) .. ok
270: Region Z:20-40 (CRAM input) .. ok
271: Count Z:20-40 (CRAM input) .. ok
272: Region ref1 (BAM input) .. ok
273: Count ref1 (BAM input) .. ok
274: Region ref1 (CRAM input) .. ok
275: Count ref1 (CRAM input) .. ok
276: Region ref1:15 (BAM input) .. ok
277: Count ref1:15 (BAM input) .. ok
278: Region ref1:15 (CRAM input) .. ok
279: Count ref1:15 (CRAM input) .. ok
280: Region ref1:15-45 (BAM input) .. ok
281: Count ref1:15-45 (BAM input) .. ok
282: Region ref1:15-45 (CRAM input) .. ok
283: Count ref1:15-45 (CRAM input) .. ok
284: Region ref1:15-45 ref2 (BAM input) .. ok
285: Count ref1:15-45 ref2 (BAM input) .. ok
286: Region ref1:15-45 ref2 (CRAM input) .. ok
287: Count ref1:15-45 ref2 (CRAM input) .. ok
288: Region ref1:15-45 ref2:16 (BAM input) .. ok
289: Count ref1:15-45 ref2:16 (BAM input) .. ok
290: Region ref1:15-45 ref2:16 (CRAM input) .. ok
291: Count ref1:15-45 ref2:16 (CRAM input) .. ok
292: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
293: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
294: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
295: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
296: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
297: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
298: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
299: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
300: Region -f 128 ref1 (BAM input) .. ok
301: Count -f 128 ref1 (BAM input) .. ok
302: Region -f 128 ref1 (CRAM input) .. ok
303: Count -f 128 ref1 (CRAM input) .. ok
304: Region -q 50 ref1:15-45 (BAM input) .. ok
305: Count -q 50 ref1:15-45 (BAM input) .. ok
306: Region -q 50 ref1:15-45 (CRAM input) .. ok
307: Count -q 50 ref1:15-45 (CRAM input) .. ok
308: Region -r grp2 ref1:15-45 (BAM input) .. ok
309: Count -r grp2 ref1:15-45 (BAM input) .. ok
310: Region -r grp2 ref1:15-45 (CRAM input) .. ok
311: Count -r grp2 ref1:15-45 (CRAM input) .. ok
312: Region * (BAM input) .. ok
313: Count * (BAM input) .. ok
314: Region * (CRAM input) .. ok
315: Count * (CRAM input) .. ok
316: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (BAM input).. ok
317: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (BAM input).. ok
318: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (CRAM input).. ok
319: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (CRAM input).. ok
320: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (BAM input).. ok
321: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (BAM input).. ok
322: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (CRAM input).. ok
323: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (CRAM input).. ok
324: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (BAM input).. ok
325: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (BAM input).. ok
326: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (CRAM input).. ok
327: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (CRAM input).. ok
328: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (BAM input).. ok
329: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (BAM input).. ok
330: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (CRAM input).. ok
331: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (CRAM input).. ok
332: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok
333: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok
334: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
335: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
336: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
337: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
338: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
339: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
340: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
341: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
342: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
343: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
344: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
345: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
346: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
347: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
348: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
349: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
350: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
351: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
352: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
353: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
354: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
355: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
356: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
357: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok
358: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
359: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok
360: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
361: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
362: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
363: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
364: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
365: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
366: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
367: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
368: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
369: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
370: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
371: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
372: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
373: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
374: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
375: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
376: Make BAM with no M5/UR tags .. ok
377: Add @SQ with -t (SAM -> SAM) .. ok
378: Add @SQ with -T (SAM -> SAM) .. ok
379: Add @SQ with -t (BAM -> SAM) .. ok
380: Add @SQ with -T (BAM -> SAM) .. ok
381: Add @SQ with -t (SAM -> BAM) .. ok
382: Add @SQ with -T (SAM -> BAM) .. ok
383: Add @SQ with -t (BAM -> BAM) .. ok
384: Add @SQ with -T (BAM -> BAM) .. ok
385: Add @SQ with -t (SAM -> CRAM) .. ok
386: Add @SQ with -T (SAM -> CRAM) .. ok
387: Add @SQ with -t (BAM -> CRAM) .. ok
388: Add @SQ with -T (BAM -> CRAM) .. ok
389: Make CRAM with no UR field .. ok
390: Decoding CRAM with no UR field via -T .. ok
391: CIGAR B-operator removal .. ok
392: Big SAM -> BAM .. ok
393: Big SAM -> BAM (2 threads) .. ok
394: Big SAM -> BAM (4 threads) .. ok
395: Big SAM -> CRAM .. ok
396: Big SAM -> CRAM (2 threads) .. ok
397: Big SAM -> CRAM (4 threads) .. ok
398: Subsample 0.2 (SAM input) ............ ok
399: Subsample 0.5 (SAM input) ............ ok
400: Subsample 0.8 (SAM input) ............ ok
401: Subsample 0.2 (BAM input) ............ ok
402: Subsample 0.5 (BAM input) ............ ok
403: Subsample 0.8 (BAM input) ............ ok
404: Subsample 0.2 (CRAM input) ............ ok
405: Subsample 0.5 (CRAM input) ............ ok
406: Subsample 0.8 (CRAM input) ............ ok
407: SAM add PG .. ok
408: Unset dup flag, remove dt and do tags .. 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/CGFKdSjwrP/bam2fq.discard.s.fq -0 /tmp/CGFKdSjwrP/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:
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/CGFKdSjwrP/bam2fq.discard.s.fq -0 /tmp/CGFKdSjwrP/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_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_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/2lQslz5iYz - /<<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/CGFKdSjwrP/merge.tag.1.bam /tmp/CGFKdSjwrP/merge.tag.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/CGFKdSjwrP/merge.tag.3.bam /tmp/CGFKdSjwrP/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/CGFKdSjwrP/merge.bed.1.bam /tmp/CGFKdSjwrP/merge.bed.2.bam
.. 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/bsw7qqXov9 - /<<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/CGFKdSjwrP/merge.tag.1.bam /tmp/CGFKdSjwrP/merge.tag.2.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/CGFKdSjwrP/merge.tag.3.bam /tmp/CGFKdSjwrP/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/CGFKdSjwrP/merge.bed.1.bam /tmp/CGFKdSjwrP/merge.bed.2.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/CGFKdSjwrP/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/CGFKdSjwrP/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/CGFKdSjwrP/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 -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 -@ 2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/CGFKdSjwrP/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/CGFKdSjwrP/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/CGFKdSjwrP/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 -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_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 -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 -O sam /<<PKGBUILDDIR>>/test/fixmate/7_two_read_mapped.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/8_isize_overflow_64bit.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 -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 -O sam /<<PKGBUILDDIR>>/test/fixmate/7_two_read_mapped.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/8_isize_overflow_64bit.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: [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: [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: [markdup] error: no MC tag. Please run samtools fixmate on file first.
[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: [markdup] error: no ms score tag. Please run samtools fixmate on file first.
[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 -@ 2 -O sam --no-PG /<<PKGBUILDDIR>>/test/markdup/1_name_sort.sam -
ERR: [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: [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: [markdup] error: no MC tag. Please run samtools fixmate on file first.
[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: [markdup] error: no ms score tag. Please run samtools fixmate on file first.
[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_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_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 -@ 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_large_positions:
/<<PKGBUILDDIR>>/samtools view -h --no-PG /tmp/CGFKdSjwrP/longref.sam.gz
.. ok
test_large_positions:
/<<PKGBUILDDIR>>/samtools view -h --no-PG /tmp/CGFKdSjwrP/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/CGFKdSjwrP/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/CGFKdSjwrP/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 -@ 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_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 | egrep -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 | egrep -v 'Samtools version|Command line'
.. ok
Number of tests:
total .. 788
passed .. 744
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 ===
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam
Expected passes: 163
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: 47
Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -fr -- /tmp/dh-xdg-rundir-qeq18XxU
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 -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
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*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o
rm -f samtools libbam.a 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 -d debian/samtools//usr
cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
install -d debian/samtools//usr/share/man
cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
install -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//
cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
install -d debian/.debhelper/generated/samtools
install -d debian/.debhelper/generated/samtools-test
# 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 -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
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
install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian
install -p -m0644 NEWS debian/samtools/usr/share/doc/samtools/changelog
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installexamples -a
install -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-coverage.1 debian/samtools/usr/share/man/man1/samtools-depad.1
man-recode --to-code UTF-8 --suffix .dh-new 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-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1
man-recode --to-code UTF-8 --suffix .dh-new 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-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1
man-recode --to-code UTF-8 --suffix .dh-new 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-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-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-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-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1
mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1
chmod 0644 -- 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-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.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-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1
mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.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-coverage.1 debian/samtools/usr/share/man/man1/samtools-depad.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-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1
mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.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
chmod 0644 -- 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-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1
dh_lintian -a
install -d debian/samtools/usr/share/lintian/overrides
install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a
(grep -a -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl:any) > debian/samtools.substvars.new
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 1635187983 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/NEWS.Debian 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-coverage.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-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-reheader.1 usr/share/man/man1/samtools-rmdup.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/NEWS.Debian 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-coverage.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-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-reheader.1 usr/share/man/man1/samtools-rmdup.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 -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 622021 new size 647298
objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug
dh_strip -a
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/95
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/95/b97ab9632a519fac614b9a6d1f687d0cadfd67.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/95/b97ab9632a519fac614b9a6d1f687d0cadfd67.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/95/b97ab9632a519fac614b9a6d1f687d0cadfd67.debug debian/samtools/usr/bin/samtools
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80/8ffdbd4de98f332424a7ecc35ee5704b9cf6ac.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80/8ffdbd4de98f332424a7ecc35ee5704b9cf6ac.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/80/8ffdbd4de98f332424a7ecc35ee5704b9cf6ac.debug debian/samtools/usr/bin/ace2sam
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d3
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d3/4a9486ea0b3b94a2bd7bc94584e9e008f950fb.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d3/4a9486ea0b3b94a2bd7bc94584e9e008f950fb.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/d3/4a9486ea0b3b94a2bd7bc94584e9e008f950fb.debug debian/samtools/usr/bin/maq2sam-long
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/11
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/11/93ff861d1c33bc30d367d8f59b54d41ef71410.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/11/93ff861d1c33bc30d367d8f59b54d41ef71410.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/11/93ff861d1c33bc30d367d8f59b54d41ef71410.debug debian/samtools/usr/bin/maq2sam-short
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4f
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4f/413998e5df5324c1b92d16b1fa810cabd3b411.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4f/413998e5df5324c1b92d16b1fa810cabd3b411.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/4f/413998e5df5324c1b92d16b1fa810cabd3b411.debug debian/samtools/usr/bin/md5fa
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/29
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/29/eb2ea7791e9940e0b65a2007b0c06b99bd4f28.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/29/eb2ea7791e9940e0b65a2007b0c06b99bd4f28.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/29/eb2ea7791e9940e0b65a2007b0c06b99bd4f28.debug debian/samtools/usr/bin/md5sum-lite
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1/9c793bd4a061aa9b0dedc5c69c4f4e180a2eab.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1/9c793bd4a061aa9b0dedc5c69c4f4e180a2eab.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/a1/9c793bd4a061aa9b0dedc5c69c4f4e180a2eab.debug debian/samtools/usr/bin/wgsim
install -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 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym
dh_makeshlibs -a
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools 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/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/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
install -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=1193ff861d1c33bc30d367d8f59b54d41ef71410 29eb2ea7791e9940e0b65a2007b0c06b99bd4f28 4f413998e5df5324c1b92d16b1fa810cabd3b411 808ffdbd4de98f332424a7ecc35ee5704b9cf6ac 95b97ab9632a519fac614b9a6d1f687d0cadfd67 a19c793bd4a061aa9b0dedc5c69c4f4e180a2eab d34a9486ea0b3b94a2bd7bc94584e9e008f950fb" -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 ${perl:Depends} unused, but is defined
chmod 0644 -- debian/samtools/DEBIAN/control
dh_md5sums -a
cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/samtools/DEBIAN/md5sums
cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --root-owner-group --build debian/samtools ..
dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root ..
dpkg-deb: building package 'samtools' in '../samtools_1.13-4_armhf.deb'.
dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.13-4_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../samtools_1.13-4_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-source: info: using options from samtools-1.13/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-10-28T07:01:24Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
samtools_1.13-4_armhf.changes:
------------------------------
Format: 1.8
Date: Mon, 25 Oct 2021 20:53:03 +0200
Source: samtools
Binary: samtools samtools-dbgsym
Architecture: armhf
Version: 1.13-4
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
samtools - processing sequence alignments in SAM, BAM and CRAM formats
Closes: 997834
Changes:
samtools (1.13-4) unstable; urgency=medium
.
* [650b7a7] d/rules: only disable executable bit if test package is built.
(Closes: #997834)
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bfe4ef5487b4b7e3847abc5aaf84a428b01346a0 5907 samtools_1.13-4_armhf.buildinfo
5faf245c3951d239337ac8517d27b66d9f398a5e 524720 samtools_1.13-4_armhf.deb
Checksums-Sha256:
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74d6390aa407df1d4dd0cf9a0a04de3c19dcd725c4aef219fd6efd75a1d10305 5907 samtools_1.13-4_armhf.buildinfo
af11296db372c134b6f40b66fcfdda6c179e7fdef06adac1b08809a559c7609b 524720 samtools_1.13-4_armhf.deb
Files:
e95e9f81359b69b3f3d642cb2c11a6dc 801228 debug optional samtools-dbgsym_1.13-4_armhf.deb
b81e142a07e7d79fb4e9c9dce1c242c6 5907 science optional samtools_1.13-4_armhf.buildinfo
711de56c2ec9e18da0b166a3f23a4efb 524720 science optional samtools_1.13-4_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
samtools-dbgsym_1.13-4_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 801228 bytes: control archive=904 bytes.
618 bytes, 12 lines control
830 bytes, 8 lines md5sums
Package: samtools-dbgsym
Source: samtools
Version: 1.13-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 873
Depends: samtools (= 1.13-4)
Section: debug
Priority: optional
Description: debug symbols for samtools
Build-Ids: 1193ff861d1c33bc30d367d8f59b54d41ef71410 29eb2ea7791e9940e0b65a2007b0c06b99bd4f28 4f413998e5df5324c1b92d16b1fa810cabd3b411 808ffdbd4de98f332424a7ecc35ee5704b9cf6ac 95b97ab9632a519fac614b9a6d1f687d0cadfd67 a19c793bd4a061aa9b0dedc5c69c4f4e180a2eab d34a9486ea0b3b94a2bd7bc94584e9e008f950fb
drwxr-xr-x root/root 0 2021-10-25 18:53 ./
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/lib/debug/.build-id/11/
-rw-r--r-- root/root 11044 2021-10-25 18:53 ./usr/lib/debug/.build-id/11/93ff861d1c33bc30d367d8f59b54d41ef71410.debug
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/lib/debug/.build-id/29/
-rw-r--r-- root/root 7352 2021-10-25 18:53 ./usr/lib/debug/.build-id/29/eb2ea7791e9940e0b65a2007b0c06b99bd4f28.debug
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/lib/debug/.build-id/4f/
-rw-r--r-- root/root 10360 2021-10-25 18:53 ./usr/lib/debug/.build-id/4f/413998e5df5324c1b92d16b1fa810cabd3b411.debug
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/lib/debug/.build-id/80/
-rw-r--r-- root/root 23036 2021-10-25 18:53 ./usr/lib/debug/.build-id/80/8ffdbd4de98f332424a7ecc35ee5704b9cf6ac.debug
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/lib/debug/.build-id/95/
-rw-r--r-- root/root 782960 2021-10-25 18:53 ./usr/lib/debug/.build-id/95/b97ab9632a519fac614b9a6d1f687d0cadfd67.debug
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/lib/debug/.build-id/a1/
-rw-r--r-- root/root 22108 2021-10-25 18:53 ./usr/lib/debug/.build-id/a1/9c793bd4a061aa9b0dedc5c69c4f4e180a2eab.debug
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/lib/debug/.build-id/d3/
-rw-r--r-- root/root 11044 2021-10-25 18:53 ./usr/lib/debug/.build-id/d3/4a9486ea0b3b94a2bd7bc94584e9e008f950fb.debug
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 3232 2021-10-25 18:53 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/share/
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-25 18:53 ./usr/share/doc/samtools-dbgsym -> samtools
samtools_1.13-4_armhf.deb
-------------------------
new Debian package, version 2.0.
size 524720 bytes: control archive=2836 bytes.
892 bytes, 18 lines control
5227 bytes, 77 lines md5sums
Package: samtools
Version: 1.13-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1124
Depends: libc6 (>= 2.29), libhts3 (>= 1.13), libncurses6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.2.3.3)
Suggests: cwltool
Breaks: bio-tradis (<= 1.4.5+dfsg-1), iva (<= 1.0.9+ds-6)
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 2021-10-25 18:53 ./
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/bin/
-rwxr-xr-x root/root 18012 2021-10-25 18:53 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5443 2021-10-25 18:53 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3360 2021-10-25 18:53 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 17996 2021-10-25 18:53 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 3300 2021-10-25 18:53 ./usr/bin/fasta-sanitize.pl
-rwxr-xr-x root/root 6121 2021-10-25 18:53 ./usr/bin/interpolate_sam.pl
-rwxr-xr-x root/root 9820 2021-10-25 18:53 ./usr/bin/maq2sam-long
-rwxr-xr-x root/root 9820 2021-10-25 18:53 ./usr/bin/maq2sam-short
-rwxr-xr-x root/root 9820 2021-10-25 18:53 ./usr/bin/md5fa
-rwxr-xr-x root/root 5724 2021-10-25 18:53 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 7969 2021-10-25 18:53 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 44331 2021-10-25 18:53 ./usr/bin/plot-ampliconstats
-rwxr-xr-x root/root 50473 2021-10-25 18:53 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3204 2021-10-25 18:53 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8957 2021-10-25 18:53 ./usr/bin/sam2vcf.pl
-rwxr-xr-x root/root 550416 2021-10-25 18:53 ./usr/bin/samtools
-rwxr-xr-x root/root 16474 2021-10-25 18:53 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11333 2021-10-25 18:53 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3905 2021-10-25 18:53 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 18052 2021-10-25 18:53 ./usr/bin/wgsim
-rwxr-xr-x root/root 12542 2021-10-25 18:53 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3579 2021-10-25 18:53 ./usr/bin/zoom2sam.pl
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/share/
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/share/commonwl/
-rwxr-xr-x root/root 1906 2021-10-24 18:24 ./usr/share/commonwl/samtools-faidx.cwl
-rwxr-xr-x root/root 1979 2021-10-24 18:24 ./usr/share/commonwl/samtools-index.cwl
-rwxr-xr-x root/root 1627 2021-10-24 18:24 ./usr/share/commonwl/samtools-rmdup.cwl
-rwxr-xr-x root/root 2834 2021-10-24 18:24 ./usr/share/commonwl/samtools-sort.cwl
-rwxr-xr-x root/root 6224 2021-10-24 18:24 ./usr/share/commonwl/samtools-view.cwl
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2021-07-07 17:18 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 369 2021-10-24 18:24 ./usr/share/doc/samtools/NEWS.Debian.gz
-rw-r--r-- root/root 497 2021-10-24 18:24 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 2480 2021-07-07 17:18 ./usr/share/doc/samtools/README.gz
-rw-r--r-- root/root 6045 2021-10-25 18:53 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 26715 2021-07-07 17:18 ./usr/share/doc/samtools/changelog.gz
-rw-r--r-- root/root 2250 2021-10-24 18:24 ./usr/share/doc/samtools/copyright
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 1315 2021-07-07 17:18 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 3225 2021-07-07 17:18 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2021-10-25 18:53 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 98 2021-07-07 17:18 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2021-07-07 17:18 ./usr/share/doc/samtools/examples/toy.sam
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/share/lintian/
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 166 2021-10-24 18:24 ./usr/share/lintian/overrides/samtools
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/share/man/
drwxr-xr-x root/root 0 2021-10-25 18:53 ./usr/share/man/man1/
-rw-r--r-- root/root 462 2021-10-25 18:53 ./usr/share/man/man1/ace2sam.1.gz
-rw-r--r-- root/root 1636 2021-10-25 18:53 ./usr/share/man/man1/samtools-addreplacerg.1.gz
-rw-r--r-- root/root 2311 2021-10-25 18:53 ./usr/share/man/man1/samtools-ampliconclip.1.gz
-rw-r--r-- root/root 5817 2021-10-25 18:53 ./usr/share/man/man1/samtools-ampliconstats.1.gz
-rw-r--r-- root/root 1877 2021-10-25 18:53 ./usr/share/man/man1/samtools-bedcov.1.gz
-rw-r--r-- root/root 2043 2021-10-25 18:53 ./usr/share/man/man1/samtools-calmd.1.gz
-rw-r--r-- root/root 1539 2021-10-25 18:53 ./usr/share/man/man1/samtools-cat.1.gz
-rw-r--r-- root/root 2301 2021-10-25 18:53 ./usr/share/man/man1/samtools-collate.1.gz
-rw-r--r-- root/root 2365 2021-10-25 18:53 ./usr/share/man/man1/samtools-coverage.1.gz
-rw-r--r-- root/root 1750 2021-10-25 18:53 ./usr/share/man/man1/samtools-depad.1.gz
-rw-r--r-- root/root 3092 2021-10-25 18:53 ./usr/share/man/man1/samtools-depth.1.gz
-rw-r--r-- root/root 1555 2021-10-25 18:53 ./usr/share/man/man1/samtools-dict.1.gz
-rw-r--r-- root/root 2083 2021-10-25 18:53 ./usr/share/man/man1/samtools-faidx.1.gz
-rw-r--r-- root/root 3564 2021-10-25 18:53 ./usr/share/man/man1/samtools-fasta.1.gz
lrwxrwxrwx root/root 0 2021-10-25 18:53 ./usr/share/man/man1/samtools-fastq.1.gz -> samtools-fasta.1.gz
-rw-r--r-- root/root 1524 2021-10-25 18:53 ./usr/share/man/man1/samtools-fixmate.1.gz
-rw-r--r-- root/root 1494 2021-10-25 18:53 ./usr/share/man/man1/samtools-flags.1.gz
-rw-r--r-- root/root 2605 2021-10-25 18:53 ./usr/share/man/man1/samtools-flagstat.1.gz
-rw-r--r-- root/root 2133 2021-10-25 18:53 ./usr/share/man/man1/samtools-fqidx.1.gz
-rw-r--r-- root/root 1410 2021-10-25 18:53 ./usr/share/man/man1/samtools-idxstats.1.gz
-rw-r--r-- root/root 3326 2021-10-25 18:53 ./usr/share/man/man1/samtools-import.1.gz
-rw-r--r-- root/root 1714 2021-10-25 18:53 ./usr/share/man/man1/samtools-index.1.gz
-rw-r--r-- root/root 3082 2021-10-25 18:53 ./usr/share/man/man1/samtools-markdup.1.gz
-rw-r--r-- root/root 3028 2021-10-25 18:53 ./usr/share/man/man1/samtools-merge.1.gz
-rw-r--r-- root/root 6376 2021-10-25 18:53 ./usr/share/man/man1/samtools-mpileup.1.gz
-rw-r--r-- root/root 1422 2021-10-25 18:53 ./usr/share/man/man1/samtools-phase.1.gz
-rw-r--r-- root/root 1675 2021-10-25 18:53 ./usr/share/man/man1/samtools-quickcheck.1.gz
-rw-r--r-- root/root 1955 2021-10-25 18:53 ./usr/share/man/man1/samtools-reheader.1.gz
-rw-r--r-- root/root 1468 2021-10-25 18:53 ./usr/share/man/man1/samtools-rmdup.1.gz
-rw-r--r-- root/root 3485 2021-10-25 18:53 ./usr/share/man/man1/samtools-sort.1.gz
-rw-r--r-- root/root 1643 2021-10-25 18:53 ./usr/share/man/man1/samtools-split.1.gz
-rw-r--r-- root/root 6198 2021-10-25 18:53 ./usr/share/man/man1/samtools-stats.1.gz
-rw-r--r-- root/root 1425 2021-10-25 18:53 ./usr/share/man/man1/samtools-targetcut.1.gz
-rw-r--r-- root/root 1627 2021-10-25 18:53 ./usr/share/man/man1/samtools-tview.1.gz
-rw-r--r-- root/root 5554 2021-10-25 18:53 ./usr/share/man/man1/samtools-view.1.gz
-rw-r--r-- root/root 14017 2021-10-25 18:53 ./usr/share/man/man1/samtools.1.gz
-rw-r--r-- root/root 410 2021-10-25 18:53 ./usr/share/man/man1/samtools.pl.1.gz
-rw-r--r-- root/root 518 2021-10-25 18:53 ./usr/share/man/man1/wgsim.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 24808
Build-Time: 205
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 276
Job: samtools_1.13-4
Machine Architecture: armhf
Package: samtools
Package-Time: 502
Source-Version: 1.13-4
Space: 24808
Status: successful
Version: 1.13-4
--------------------------------------------------------------------------------
Finished at 2021-10-28T07:01:24Z
Build needed 00:08:22, 24808k disk space