[med-svn] [Git][med-team/samtools][master] 6 commits: d/watch: version=5
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Sep 16 14:11:27 BST 2026
Andreas Tille pushed to branch master at Debian Med / samtools
Commits:
dd843e92 by Andreas Tille at 2026-09-16T14:47:39+02:00
d/watch: version=5
- - - - -
9c996e8b by Andreas Tille at 2026-09-16T14:54:48+02:00
d/copyright: review; Add d/lrc.config
- - - - -
d5c2997e by Andreas Tille at 2026-09-16T13:55:06+01:00
Remove redundant Priority: optional from source stanza.
Changes-By: lintian-brush
Fixes: lintian: source: redundant-priority-optional-field
See-also: https://lintian.debian.org/tags/redundant-priority-optional-field.html
- - - - -
5e3a6ce9 by Andreas Tille at 2026-09-16T13:55:06+01:00
Update standards version to 4.7.4, no changes needed.
Upgrade checklist verified:
4.7.3 → 4.7.4:
* Package is not in non-free-firmware
Changes-By: lintian-brush
Fixes: lintian: source: out-of-date-standards-version 4.7.2 (released 2025-02-27) (current is 4.7.4.1)
See-also: https://lintian.debian.org/tags/out-of-date-standards-version.html
- - - - -
93014a15 by Andreas Tille at 2026-09-16T14:59:37+02:00
Update changelog
- - - - -
fcf9fe1d by Andreas Tille at 2026-09-16T15:11:16+02:00
cme fix dpkg-control
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/lrc.config
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+samtools (1.22.1-2) UNRELEASED; urgency=medium
+
+ * d/watch: version=5
+ * d/copyright: review
+ * Add d/lrc.config
+ * Remove redundant Priority: optional from source stanza.
+ * Update standards version to 4.7.4, no changes needed.
+ * cme fix dpkg-control
+
+ -- Andreas Tille <tille at debian.org> Wed, 16 Sep 2026 14:59:09 +0200
+
samtools (1.22.1-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,24 +1,25 @@
Source: samtools
+# tabix is needed for the regression tests.
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>,
- Étienne Mollier <emollier at debian.org>
+Uploaders:
+ Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>,
Section: science
-Priority: optional
-Build-Depends: debhelper-compat (= 13),
- bash-completion,
- libio-pty-perl <!nocheck>,
- libncurses-dev,
- libhts-dev (>= 1.22~),
- zlib1g-dev,
- automake,
- autoconf-archive,
- pkgconf,
- tabix,
- liblzma-dev,
- libbz2-dev
-# tabix is needed for the regression tests.
-Standards-Version: 4.7.2
+Build-Depends:
+ debhelper-compat (= 14),
+ bash-completion,
+ libio-pty-perl <!nocheck>,
+ libncurses-dev,
+ libhts-dev (>= 1.22~),
+ zlib1g-dev,
+ automake,
+ autoconf-archive,
+ pkgconf,
+ tabix,
+ liblzma-dev,
+ libbz2-dev,
Vcs-Browser: https://salsa.debian.org/med-team/samtools
Vcs-Git: https://salsa.debian.org/med-team/samtools.git
Homepage: https://www.htslib.org/
@@ -27,9 +28,11 @@ Rules-Requires-Root: no
Package: samtools
Architecture: any
# older iva & bio-tradis have bad samtools version parsing code
-Depends: ${shlibs:Depends},
- ${misc:Depends}
-Suggests: cwltool
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+Suggests:
+ cwltool,
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
@@ -41,8 +44,10 @@ Description: processing sequence alignments in SAM, BAM and CRAM formats
Package: samtools-test
Architecture: all
Multi-Arch: foreign
-Depends: ${misc:Depends}
-Recommends: libio-pty-perl
+Depends:
+ ${misc:Depends},
+Recommends:
+ libio-pty-perl,
Description: test files for the samtools package
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format.
=====================================
debian/copyright
=====================================
@@ -10,6 +10,32 @@ Copyright: © 2008–2024, Genome Research Ltd. (GRL)
© 2012–2013 Peter Cock, The James Hutton Institute.
License: Expat
+Files: lz4/*
+Copyright: 2011-2017, Yann Collet.
+License: BSD-2-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+ .
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following disclaimer
+ in the documentation and/or other materials provided with the
+ distribution.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
Files: debian/*.cwl
Copyright: the CWL project
License: Apache-2.0
=====================================
debian/lrc.config
=====================================
@@ -0,0 +1,4 @@
+install-sh
+m4/ax_with_htslib.m4
+m4/hts_prog_cc_warnings.m4
+debian/ax_with_htslib.m4
=====================================
debian/watch
=====================================
@@ -1,3 +1,5 @@
-version=4
-opts=filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/samtools-$1\.tar\.gz/,uversionmangle=s/-rc/~rc/ \
- https://github.com/samtools/samtools/tags .*/v?(\d\S*)\.tar\.gz
+Version: 5
+
+Template: Github
+Dist: https://github.com/samtools/samtools
+Uversionmangle: s/-rc/~rc/
View it on GitLab: https://salsa.debian.org/med-team/samtools/-/compare/9d877a90563348c5be95b8aeb0b5253107ecfd0b...fcf9fe1da871e07e9044e1920763871fce31979e
--
View it on GitLab: https://salsa.debian.org/med-team/samtools/-/compare/9d877a90563348c5be95b8aeb0b5253107ecfd0b...fcf9fe1da871e07e9044e1920763871fce31979e
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