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
