bedtools (2.31.1+dfsg-2) unstable; urgency=medium * d/clean: new: remove test/getfasta/t.fa.gz.gzi. (Closes: #1043957) -- Étienne Mollier Mon, 04 Dec 2023 20:13:11 +0100 bedtools (2.31.1+dfsg-1) unstable; urgency=medium * New upstream version 2.31.1+dfsg * gcc-13.patch: remove: applied upstream. -- Étienne Mollier Fri, 24 Nov 2023 12:10:46 +0100 bedtools (2.31.0+dfsg-2) unstable; urgency=medium * gcc-13.patch: fixed upstream by different change. The Applied-Upstream field is set accordingly to point to PR 1067. * d/rules: use sse for floating point calculations. This fixes bedtools "intersect" test failures during build time. This change is brought for consistency with htslib's own settings. While this is an architecture baseline violation, the alternative is no htslib support at all for the i386 distribution, since it fails its own test suite with anything else than sse for floating point calculations. (Closes: #1055414) * d/control: depend on python3:any per M-A hint. -- Étienne Mollier Sat, 18 Nov 2023 16:34:59 +0100 bedtools (2.31.0+dfsg-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.6.2 (routine-update) * remove_barski_binding_site.png.patch: unfuzz. * 2to3.patch: refresh. * 2to3.patch: declare forwarding not-needed. Upstream looks to assume compatibility with both python and python3. * 2to3.patch: remove further occurrences of python. There are some tests and some documentation referring to the unversioned python, which in Debian is by default python2. * hardening patch: unfuzz. * htsutil patch: unfuzz. * gcc-13.patch: add; fix ftbfs with gcc-13. Thanks to David Seifert (Closes: #1037588) * d/control: bedtools-test depend on python3. -- Étienne Mollier Fri, 23 Jun 2023 22:57:16 +0200 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Sat, 05 Nov 2016 21:48:09 +0900 bedtools (2.26.0+dfsg-2) unstable; urgency=medium * Enable reproducible builds Closes: #834110 -- Andreas Tille 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 (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 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 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 ) Closes: #791830 -- Andreas Tille 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 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 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 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 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 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 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 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 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 Wed, 11 Jan 2012 15:07:45 +0900 bedtools (2.14.3-1) unstable; urgency=low 04f6aa3 Bugfix release. -- Charles Plessy Fri, 04 Nov 2011 09:25:38 +0900 bedtools (2.14.2-1) unstable; urgency=low 356313d Bugfix release. -- Charles Plessy 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 Thu, 03 Nov 2011 11:14:35 +0900 bedtools (2.13.4-1) unstable; urgency=low e553c37 New upstream release. -- Charles Plessy 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 Mon, 17 Oct 2011 21:30:47 +0100 bedtools (2.13.3-1) unstable; urgency=low ea1c596 New upstream release. -- Charles Plessy Wed, 05 Oct 2011 17:18:15 +0900 bedtools (2.13.2-1) unstable; urgency=low 1930a26 New upstream release. -- Charles Plessy 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 Sat, 10 Sep 2011 23:32:43 +0900 bedtools (2.12.0-1) unstable; urgency=low * Initial release (Closes: #629597) -- Charles Plessy Wed, 08 Jun 2011 17:01:19 +0900