* Add d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch in support
of fixing 'zlib: compressBound() returns an incorrect result on z15'.
(LP: #1961427)
[ 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)
[ 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.
* Team upload.
* Repair broken link in run-unit-test script; fixes autopkgtest regression.
* 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
[ 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)
* Team upload.
* Build on any architecture
[ 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
* 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
* 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.
* Team upload.
* New upstream version
* Removed Chris' reproducible builds patch - upstream diverged too much
* Use 2to3 to port to Python3
Closes: #936199
* Remove unsafe links for gcc and g++
* Team upload.
* And another new dependency on liblzma-dev
* Team upload.
* Debian CI kindly pointed me to a new build dependency
on libbz2-dev (https://salsa.debian.org/med-team/bedtools/-/jobs/238984).
* 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.
* Disable the shuffle test on other 32-bit architectures.
* Restrict build to little-endian release architectures. Closes: #890117
* QA-build with Salsa.
* 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
* 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
* New upstream version
* cme fix dpkg-control
* debhelper 11
* d/rules: do not parse d/changelog
* Use "override_dh_install-indep" to prevent failures when
architecture-independent packages are not built. Closes: #876802
[ 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).
d6d3452 Sync with upstream repo at commit 6bf23c, closes: #831833.
* Enable reproducible builds
Closes: #834110
[ 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
e37865 Merge tag 'v2.25.0' into debian/unstable
* 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
[ 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
856a5fd Merge tag 'v2.21.0' into debian/unstable
a4f6ab7 Merge corrections on version number.
* New upstream version
* Fix permission of some genome example files
* 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
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
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.
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.
b7f2405 New upstream release.
4add346 Corrected, updated and normalised Debian copyright.
00b426d Conforms to Debian Policy 3.9.3.
72c3c94 Verbose Debhelper.
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.
04f6aa3 Bugfix release.
356313d Bugfix release.
bce732c New upstream release and new tool, multiBedIntersect.
e553c37 New upstream release.
* Pre-Depends: dpkg (>= 1.15.6) for xz compression support. Needed until
after Ubuntu 12.04 LTS.
ea1c596 New upstream release.
1930a26 New upstream release.
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.
* Initial release (Closes: #629597)