bedtools (2.31.1+dfsg-2) unstable; urgency=medium

  * d/clean: new: remove test/getfasta/t.fa.gz.gzi. (Closes: #1043957)

 -- Étienne Mollier <emollier@debian.org>  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 <emollier@debian.org>  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 <emollier@debian.org>  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 <emollier@debian.org>  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 <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

# Older entries have been removed from this changelog.
# To read the complete changelog use `apt changelog bedtools`.
