bedtools (2.30.0+dfsg-3) unstable; urgency=medium
* Do not use ulimit in test
Closes: #1034349
* Override false positive (see lintian bug #1017966)
-- Andreas Tille <tille@debian.org> Thu, 13 Apr 2023 14:12:15 +0200
bedtools (2.30.0+dfsg-2) unstable; urgency=medium
[ Steffen Möller ]
* Update metadata - indent, added ref to guix
[ Étienne Mollier ]
* d/control: add myself to uploaders
* d/watch: fix broken link to github
[ Andreas Tille ]
* Standards-Version: 4.6.0 (routine-update)
-- Andreas Tille <tille@debian.org> Thu, 02 Sep 2021 06:54:44 +0200
bedtools (2.30.0+dfsg-1) unstable; urgency=medium
[ Étienne Mollier ]
* Team upload.
* New upstream version 2.30.0+dfsg.
* Refresh 2to3.patch and hardening patch.
* Remove test related patches, 32-bit-fixes.patch and spelling patch;
applied upstream.
* Do not include htsutil as a side test program in bedtools anymore;
the test tool is inlined as subcommand to reduce memory footprint.
[ John Marshall ]
* Add htsutil patch to implement the bedtools htsutil subcommand.
[ Étienne Mollier ]
* d/rules: set $htsutil to use the bedtools htsutil subcommand.
* d/t/run-unit-test: use the bedtools htsutil subcommand.
-- Étienne Mollier <etienne.mollier@mailoo.org> Wed, 27 Jan 2021 17:26:26 +0100
bedtools (2.29.2+dfsg-6) unstable; urgency=medium
* Team upload.
* Repair broken link in run-unit-test script; fixes autopkgtest regression.
-- Étienne Mollier <etienne.mollier@mailoo.org> Sun, 17 Jan 2021 12:11:39 +0100
bedtools (2.29.2+dfsg-5) unstable; urgency=medium
* Delete standard debian/gbp.conf
* Revert deletion of test binary htsutil since it is needed to replace
samtools that's not working any more for this purpose
* Move htsutil tool to bedtools package
Closes: #978679
-- Andreas Tille <tille@debian.org> Mon, 04 Jan 2021 13:01:58 +0100
bedtools (2.29.2+dfsg-4) unstable; urgency=medium
[ Michael R. Crusoe ]
* Team upload.
* Remove the need for samtools via patch from upstream.
* Include patch from Bernhard Übelacker to fix 32-bit builds. TODO: the
autopkgtests do not yet pass on i386 (and likely neither on other 32-bit
archs).
Closes: #955403
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
[ Andreas Tille ]
* Fix permissions of .sam files
* Delete test binary to make sure it will not be installed
* DEP3
* Standards-Version: 4.5.1 (routine-update)
-- Andreas Tille <tille@debian.org> Sun, 20 Dec 2020 19:03:35 +0100
bedtools (2.29.2+dfsg-3) unstable; urgency=medium
* Team upload.
* Build on any architecture
-- Michael R. Crusoe <michael.crusoe@gmail.com> Fri, 14 Feb 2020 16:02:39 +0100
bedtools (2.29.2+dfsg-2) unstable; urgency=medium
[ Steffen Moeller ]
* Team upload.
* Added version to dependency of samtools
[ Michael R. Crusoe ]
* Make the build verbose
* Fix a spelling typo
* Improve hardening & enable cross building
-- Michael R. Crusoe <michael.crusoe@gmail.com> Tue, 11 Feb 2020 16:30:06 +0100
bedtools (2.29.2+dfsg-1) unstable; urgency=medium
* Team upload.
* New upstream version
* Fixed failing intersect.new #78 test as instructed on
https://github.com/arq5x/bedtools2/issues/814
* Standard-Version: 4.5.0
-- Steffen Moeller <moeller@debian.org> Sat, 18 Jan 2020 01:44:47 +0100
bedtools (2.29.0+dfsg-2) unstable; urgency=medium
* Fix Build-Depends (s/python/python3/) and replace remaining references
to python by python3
Closes: #936199
* autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
* Remove patches louder, reproducible_build.patch that are missing
from debian/patches/series.
* Set fields Upstream-Contact in debian/copyright.
* Remove obsolete fields Contact, Name from debian/upstream/metadata.
-- Andreas Tille <tille@debian.org> Thu, 05 Dec 2019 12:11:59 +0100
bedtools (2.29.0+dfsg-1) unstable; urgency=medium
* Team upload.
* New upstream version
* Removed Chris' reproducible builds patch - upstream diverged too much
-- Steffen Moeller <moeller@debian.org> Tue, 05 Nov 2019 21:41:22 +0100
bedtools (2.28.0+dfsg1-1) unstable; urgency=medium
* Use 2to3 to port to Python3
Closes: #936199
* Remove unsafe links for gcc and g++
-- Andreas Tille <tille@debian.org> Sun, 01 Sep 2019 11:14:59 +0200
bedtools (2.28.0+dfsg-3) unstable; urgency=medium
* Team upload.
* And another new dependency on liblzma-dev
-- Steffen Moeller <moeller@debian.org> Fri, 26 Jul 2019 19:06:23 +0200
bedtools (2.28.0+dfsg-2) unstable; urgency=medium
* Team upload.
* Debian CI kindly pointed me to a new build dependency
on libbz2-dev (https://salsa.debian.org/med-team/bedtools/-/jobs/238984).
-- Steffen Moeller <moeller@debian.org> Fri, 26 Jul 2019 18:38:06 +0200
bedtools (2.28.0+dfsg-1) unstable; urgency=medium
* Team upload.
* New upstream version
* debhelper-compat 12
* Standards-Version: 4.4.0
* Semi-automated update with Andreas' routine-update script,
only reintroduced the conflicts of the test package with earlier
releases of bedtools.
-- Steffen Moeller <moeller@debian.org> Fri, 26 Jul 2019 17:33:35 +0200
bedtools (2.27.1+dfsg-4) unstable; urgency=medium
* Disable the shuffle test on other 32-bit architectures.
* Restrict build to little-endian release architectures. Closes: #890117
* QA-build with Salsa.
-- Charles Plessy <plessy@debian.org> Thu, 14 Feb 2019 22:11:21 +0900
bedtools (2.27.1+dfsg-3) unstable; urgency=medium
* Team upload.
* Print compilation commands
* For *i386: use -ffloat-store; disable shuffle tests. Closes: #890116
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
* Remove trailing whitespace in debian/changelog
* Remove trailing whitespace in debian/copyright
* mark bedtools-test as Multi-Arch: foreign
-- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 04 Feb 2019 05:33:48 -0800
bedtools (2.27.1+dfsg-2) unstable; urgency=medium
* Team upload
[ Andreas Tille ]
* Install autopkgtest script as /usr/share/doc/bedtools/run-unit-test
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
* Drop useless get-orig-source target
[ Liubov Chuprikova ]
* Fix "autopkgtest fails while it succeeded in the past"
updated run-unit-test to match new upstream tests
Closes: #894781
-- Liubov Chuprikova <chuprikovalv@gmail.com> Tue, 22 May 2018 21:31:56 +0200
bedtools (2.27.1+dfsg-1) unstable; urgency=medium
* New upstream version
* cme fix dpkg-control
* debhelper 11
* d/rules: do not parse d/changelog
-- Andreas Tille <tille@debian.org> Sat, 10 Feb 2018 10:54:56 +0100
bedtools (2.26.0+dfsg-5) unstable; urgency=medium
* Use "override_dh_install-indep" to prevent failures when
architecture-independent packages are not built. Closes: #876802
-- Charles Plessy <plessy@debian.org> Tue, 26 Sep 2017 22:42:08 +0900
bedtools (2.26.0+dfsg-4) unstable; urgency=medium
[ Andreas Tille ]
* Fix autopkgtest
* Ignore failures in the split feature for the moment
(Related to bug #747337 but hesitating to close it)
* debhelper 10
* d/watch: version=4
[Steffen Moeller]
* debian/upstream/metadata: Added references to registries
* debian/copyright: Added Upstream-Name
[ Charles Plessy ]
* Distribute /usr/bin/groupBy again.
* Conflict/Replace/Provide filo (which is being removed from Debian).
-- Charles Plessy <plessy@debian.org> Mon, 25 Sep 2017 23:09:53 +0900
bedtools (2.26.0+dfsg-3) unstable; urgency=medium
d6d3452 Sync with upstream repo at commit 6bf23c, closes: #831833.
-- Charles Plessy <plessy@debian.org> Sat, 05 Nov 2016 21:48:09 +0900
bedtools (2.26.0+dfsg-2) unstable; urgency=medium
* Enable reproducible builds
Closes: #834110
-- Andreas Tille <tille@debian.org> Fri, 12 Aug 2016 15:04:19 +0200
bedtools (2.26.0+dfsg-1) unstable; urgency=medium
[ Charles Plessy ]
854dcc2 Merge tag 'v2.26.0' into debian/unstable
99afd11 Ensure the architecture-independent package can be built separately.
Thanks to Santiago Vila <sanvila@debian.org> (Closes: #805998)
[ Andreas Tille ]
* Switch to default repository layout
* Remove docs/content/images/tool-glyphs/barski_binding_site.png from upstream
tarball since it is from
Jothi et al, 2008, doi:10.1093/nar/gkn488
since it is licensed under no-DFSG CC-BY-NC 2.0
* Delete reference to removed image from Debian shipped doc
* cme fix dpkg-control
* cme fix dpkg-copyright
* hardening += all
* drop outdated Homepage field from debian/upstream/metadata
* debian/control: Fix homepage
-- Charles Plessy <plessy@debian.org> Thu, 07 Jul 2016 13:58:08 +0900
bedtools (2.25.0-1) unstable; urgency=medium
e37865 Merge tag 'v2.25.0' into debian/unstable
-- Charles Plessy <plessy@debian.org> Fri, 04 Sep 2015 16:55:21 +0200
bedtools (2.24.0-2) unstable; urgency=medium
* Tests need bgzip from tabix package
* Add missing input files for tests
* link to genomes files in autopkgtests to enable more tests passing
* Fix MIPS build issue (Thanks for picking the patch from upstream
Arturo Borrero Gonzalez <arturo.borrero.glez@gmail.com>)
Closes: #791830
-- Andreas Tille <tille@debian.org> Thu, 16 Jul 2015 14:33:38 +0200
bedtools (2.24.0-1) unstable; urgency=medium
[ Charles Plessy ]
b757049 Merge tag 'v2.22.1' into debian/unstable
f62bafa Conforms to Policy 3.9.6.
[ Andreas Tille ]
* Remove superfluous debian/README.source and replace it by a helpful
one describing the workflow of this Git archive
* New upsteam version
* Bash completions now go to /usr/share/bash-completion/completions
* Strip executable flag from all *.bed files
* Make sure all *.sh scripts of the test suite have a proper '#!/bin/bash'
line and the executable flag set
* debian/copyright
- update download location
- turn DEP5 incompatible License field in header into a Comment
-- Andreas Tille <tille@debian.org> Tue, 07 Jul 2015 18:21:22 +0200
bedtools (2.21.0-1) unstable; urgency=medium
856a5fd Merge tag 'v2.21.0' into debian/unstable
a4f6ab7 Merge corrections on version number.
-- Charles Plessy <plessy@debian.org> Tue, 23 Sep 2014 18:48:17 +0900
bedtools (2.20.1-1) unstable; urgency=medium
* New upstream version
* Fix permission of some genome example files
-- Andreas Tille <tille@debian.org> Fri, 06 Jun 2014 21:50:39 +0200
bedtools (2.19.1-2) unstable; urgency=medium
* debian/tests/control: Add "Depends: @, samtools" as advised in
#747337
* debian/tests/upstream: Use content from bedtools-test package to
actually run the test suite
Closes: #747337
* debian/rules: Use dh to easily enable unit tests at package build
time
* Build-Depends: samtools to run the full test suite
-- Andreas Tille <tille@debian.org> Fri, 09 May 2014 09:48:05 +0200
bedtools (2.19.1-1) unstable; urgency=medium
479e63b Merge tag 'v2.19.1' into debian/unstable
[ Charles Plessy ]
93a7cf1 Create autopkgtest testsuite and a new package bedtools-test.
46183f8 debian/copyright: update path, correct license short name.
4fd441a debian/rules: removed obsolete exception of compression.
[ James McCoy ]
b4fa8e1 Move debian/upstream to debian/upstream/metadata
-- Charles Plessy <plessy@debian.org> Fri, 21 Mar 2014 14:51:44 +0900
bedtools (2.19.0-1) unstable; urgency=low
e07e70c Imported Upstream version 2.19.0
afdc61a Watch GitHub at https://github.com/arq5x/bedtools2.
4abe14e Source control file normalised with config-model-edit.
0518353 Corrected a typo in the long description. (Closes: #714873)
f63d85e Follow the layout of the upstream repository.
c25f9e5 Correct name of README file in debian/docs.
5561c7c Emulate source format 1.0 in the format 3.0 (quilt).
a45a0ab Canonical VCS URLs.
4459dfe Conforms with Policy 3.9.5.
-- Charles Plessy <plessy@debian.org> Sat, 15 Feb 2014 19:39:23 +0900
bedtools (2.17.0-1) unstable; urgency=low
bb9012e Imported Upstream version 2.16.2.
9006b23 Imported Upstream version 2.17.0.
9112569 Documented BEDTools license as a whole.
325689c Removed Pre-Depends: dpkg (>= 1.15.6).
a781b14 Conforms with Policy 3.9.4.
84b1167 Use Debhelper 9.
0bf572d Distribute the test suite.
422cd34 Bash completion for BEDTools.
-- Charles Plessy <plessy@debian.org> Sun, 04 Nov 2012 17:59:41 +0900
bedtools (2.16.1-1) unstable; urgency=low
b7f2405 New upstream release.
4add346 Corrected, updated and normalised Debian copyright.
00b426d Conforms to Debian Policy 3.9.3.
72c3c94 Verbose Debhelper.
-- Charles Plessy <plessy@debian.org> Fri, 16 Mar 2012 19:06:49 +0900
bedtools (2.15.0-1) unstable; urgency=low
3f8e754 Upstream version 2.15.0.
f27b295 Build-depend on python because of scripts/makeBashScripts.py.
2e3e8e8 Removed the /usr/bin/groupBy wrapper, as groupBy is also
distributed by the filo package.
-- Charles Plessy <plessy@debian.org> Wed, 11 Jan 2012 15:07:45 +0900
bedtools (2.14.3-1) unstable; urgency=low
04f6aa3 Bugfix release.
-- Charles Plessy <plessy@debian.org> Fri, 04 Nov 2011 09:25:38 +0900
bedtools (2.14.2-1) unstable; urgency=low
356313d Bugfix release.
-- Charles Plessy <plessy@debian.org> Thu, 03 Nov 2011 12:15:32 +0900
bedtools (2.14.1-1) unstable; urgency=low
bce732c New upstream release and new tool, multiBedIntersect.
-- Charles Plessy <plessy@debian.org> Thu, 03 Nov 2011 11:14:35 +0900
bedtools (2.13.4-1) unstable; urgency=low
e553c37 New upstream release.
-- Charles Plessy <plessy@debian.org> Sat, 29 Oct 2011 11:08:02 +0900
bedtools (2.13.3-1ubuntu1) precise; urgency=low
* Pre-Depends: dpkg (>= 1.15.6) for xz compression support. Needed until
after Ubuntu 12.04 LTS.
-- Colin Watson <cjwatson@ubuntu.com> Mon, 17 Oct 2011 21:30:47 +0100
bedtools (2.13.3-1) unstable; urgency=low
ea1c596 New upstream release.
-- Charles Plessy <plessy@debian.org> Wed, 05 Oct 2011 17:18:15 +0900
bedtools (2.13.2-1) unstable; urgency=low
1930a26 New upstream release.
-- Charles Plessy <plessy@debian.org> Sat, 24 Sep 2011 09:34:29 +0900
bedtools (2.13.1-1) unstable; urgency=low
2e3fe5e New upstream release.
ff5450e Compress source and binary packages with xz.
ef58a33 Suggest filo for the groupBy command.
df206c0 Mangle debian/watch download URL.
2fe7cff Simplified repacking as upstream tarballs do not contain
‘*/*DS_Store’ files anymore.
-- Charles Plessy <plessy@debian.org> Sat, 10 Sep 2011 23:32:43 +0900
bedtools (2.12.0-1) unstable; urgency=low
* Initial release (Closes: #629597)
-- Charles Plessy <plessy@debian.org> Wed, 08 Jun 2011 17:01:19 +0900