htslib (1.11-4) unstable; urgency=medium

  * libhts3: Breaks+Replaces: libhts-dev (<< 1.11-3). Closes: #978094

 -- Michael R. Crusoe <crusoe@debian.org>  Sat, 02 Jan 2021 16:28:22 +0100

htslib (1.11-3) unstable; urgency=medium

  [ Andreas Tille ]
  * No need to patch when using proper configure options
  * Install man5 as user rather than developer documentation
  * Fix description of tabix package
    Closes: #922860
  * Standards-Version: 4.5.1 (routine-update)
  * Update renamed lintian tag names in lintian overrides.
  * Somehow installation of htslib dir has changed

  [ Michael R. Crusoe ]
  * debian/upstream/metadata: add new pre-print

 -- Andreas Tille <tille@debian.org>  Thu, 24 Dec 2020 10:34:35 +0100

htslib (1.11-2) unstable; urgency=medium

  * Enable plugins
    Closes: #971542
  * Add missing Depends: libcurl4-gnutls-dev, libdeflate-dev
  * Fix run-unit-test script
  * Fix autopkgtest

 -- Andreas Tille <tille@debian.org>  Mon, 05 Oct 2020 09:30:04 +0200

htslib (1.11-1) unstable; urgency=medium

  * New upstream version

 -- Andreas Tille <tille@debian.org>  Thu, 01 Oct 2020 15:29:49 +0200

htslib (1.10.2-5) unstable; urgency=medium

  * debhelper-compat 13 (routine-update)
  * Add salsa-ci file (routine-update)
  * Remove default debian/gbp.conf
  * Install bgzip.1 manpage
  * Workaround issue with dh_missing

 -- Andreas Tille <tille@debian.org>  Mon, 03 Aug 2020 13:19:08 +0200

htslib (1.10.2-4) unstable; urgency=medium

  * d/control: Added Rules-Requires-Root: no
  * Exported cram_to_bam function to compile sambamba, borrowed from
    http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics
    htslib-add-cram_to_bam.patch

 -- Steffen Moeller <moeller@debian.org>  Sat, 04 Jul 2020 14:04:35 +0200

htslib (1.10.2-3) unstable; urgency=medium

  [ Andreas Tille ]
  * d/copyright: Add Upstream-Contact

  [ Michael R. Crusoe ]
  * Patch from upstream for big-endian systems. Closes: #947462
  * Mark htslib-tests as Multi-Arch: foreign
  * Standards-Version: 4.5.0 (routine-update)
  * Set upstream metadata fields: Bug-Submit.
  * add Build-Depends-Package: libhts-dev to debian/libhts3.symbols
  * debian/rules: add hack to autoconf not forget MMAP with cross building
  * pass the same flags to test and install as build
  * debian/rules: match upstream's default flags
  * debian/libhts3.symbols: remove erronously exported symbols

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Thu, 13 Feb 2020 19:25:04 +0100

htslib (1.10.2-2) unstable; urgency=medium

  * htslib-test: breaks+replaces libhts-private-dev
  * libhts3: breaks libtabixpp << 1.0.0-5

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sat, 21 Dec 2019 14:15:05 -0700

htslib (1.10.2-1) unstable; urgency=medium

  * New upstream version
  * debian/source/options: ignore changes to aclocal.m4 config.h.in configure
  * debian/control: remove libhts-private-dev (Closes: #947066)

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 20 Dec 2019 09:57:05 -0800

htslib (1.10.1-2) unstable; urgency=medium

  * Fix binary-arch vs binary-indep builds

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 18 Dec 2019 12:54:51 +0100

htslib (1.10.1-1) unstable; urgency=medium

  * New upstream version
  * for some very strange reason /usr/include/htslib/cram/cram.h is using the
    private interface header.h.  This is provided now in the
    libhts-private-dev package rather than htslib-test
  * debhelper-compat 12
  * DEB_BUILD_OPTIONS allow override_dh_auto_test
  * Remove trailing whitespace in debian/rules
  * More verbose error reporting in case of failed tests
  * Fix Perl interpreter path
  * Fix permissions of script

 -- Andreas Tille <tille@debian.org>  Tue, 17 Dec 2019 14:38:13 +0100

htslib (1.10-2) unstable; urgency=medium

  * Fix check for config.mk.
  * Simplified arch-independent build
  * libhts2 -> libhts3 to match the new SONAME
  * Update the symbols as well

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 13 Dec 2019 11:04:33 +0100

htslib (1.10-1) unstable; urgency=medium

  * New upstream release.
  * Remove build path from packaged config.mk to make the build more reproducible.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Mon, 09 Dec 2019 19:40:15 +0100

htslib (1.9-12) unstable; urgency=medium

  * Fix for the autopkgtest on i386 means we can re-enable it! (Closes: #942580)

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Mon, 09 Dec 2019 19:06:02 +0100

htslib (1.9-11) unstable; urgency=medium

  * Install README at request of upstream
  * Stop building on any-i386
    Closes: #927353

 -- Andreas Tille <tille@debian.org>  Wed, 24 Apr 2019 08:51:48 +0200

htslib (1.9-10) unstable; urgency=medium

  * Bring the libdeflate, GCS, and S3 updates back to unstable.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 16 Jan 2019 05:23:22 -0800

htslib (1.9-10~1libdeflate) experimental; urgency=medium

  * Enable GCS and AWS S3 backends.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 16 Jan 2019 00:27:21 -0800

htslib (1.9-10~0libdeflate) experimental; urgency=medium

  * Try libdeflate again.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 15 Jan 2019 07:01:58 -0800

htslib (1.9-9) unstable; urgency=medium

  * Bring the ppc64el & i386 pkg-config enhancements to unstable.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 15 Jan 2019 06:13:44 -0800

htslib (1.9-9~floatingpoint0) experimental; urgency=low

  * add SSE flags for i386 to the pkg-config.
  * Try the ppc64el targeted floating point patch again & re-enable -O2

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 02 Jan 2019 06:34:33 -0800

htslib (1.9-8) unstable; urgency=medium

  * Disable optimization on ppc64el to unblock this and many other packages
    migration to testing.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Mon, 31 Dec 2018 07:08:13 -0800

htslib (1.9-7) unstable; urgency=medium

  * Bring i386 build enhancements to unstable.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 19 Dec 2018 07:30:24 -0800

htslib (1.9-7~1~i386~1) experimental; urgency=medium

  * Turn on SSE for i386, as suggested at
    https://github.com/samtools/htslib/issues/565#issuecomment-448028771

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 18 Dec 2018 00:27:40 -0800

htslib (1.9-7~0~i386~gcc7~1) experimental; urgency=medium

  * Try dropping to gcc-7 on i386*

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Mon, 10 Dec 2018 18:02:16 -0800

htslib (1.9-6) unstable; urgency=medium

  * Revert libdeflate for DEFLATE based (de)compression and its crc32
    implementation.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 05 Dec 2018 22:59:23 -0800

htslib (1.9-5) unstable; urgency=medium

  * Add libdeflate for DEFLATE based (de)compression and its crc32
    implementation.
  * Re-add mipsel to tabix & libhts-dev as well. (Closes: #915404)

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 04 Dec 2018 20:56:12 -0800

htslib (1.9-4) unstable; urgency=medium

  * Add Breaks: python-pysam (<< 0.15~), python3-pysam (<< 0.15~)
    (Thanks to Graham Inggs <ginggs@debian.org>)
    Closes: #911492

 -- Andreas Tille <tille@debian.org>  Sun, 02 Dec 2018 07:54:46 +0100

htslib (1.9-3) unstable; urgency=medium

  * debian/control: drop *i386. Closes: #905438.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 14 Oct 2018 09:53:04 -0700

htslib (1.9-2) unstable; urgency=medium

  * Depends: zlib1g-dev
    Closes: #908501
  * Remove unused lintian overrides
  * Standards-Version: 4.2.1

 -- Andreas Tille <tille@debian.org>  Wed, 12 Sep 2018 21:22:18 +0200

htslib (1.9-1) experimental; urgency=medium

  * Team upload.

  * New upstream version. Some symbols were added, others were removed:
    - cram_to_bam was removed
    - fai_build_core was removed
  * Updated symbols list
  * Introduced -flto

 -- Steffen Moeller <moeller@debian.org>  Thu, 26 Jul 2018 18:54:12 +0200

htslib (1.8-1) experimental; urgency=medium

  * New upstream version
  * Point Vcs fields to salsa.debian.org
  * Standards-Version: 4.1.4
  * debhelper 11
  * Fix symbols file.
    Note: version 1.8 drops symbol cram_nop_decode_reset without bumping
    soversion but this should be no issue according to upstream
    (https://github.com/samtools/htslib/issues/695)

 -- Andreas Tille <tille@debian.org>  Fri, 27 Apr 2018 17:16:43 +0200

htslib (1.7-2) unstable; urgency=medium

  * Move all needed files into htslib-test package
    Closes: #890303
  * Document how to test the package
  * Update symbols file

 -- Andreas Tille <tille@debian.org>  Wed, 14 Feb 2018 13:13:18 +0100

htslib (1.7-1) unstable; urgency=medium

  * Team upload.

  * New upstream version.
  * Standards-Version: 4.1.3

  * win/* files no longer in upstream source tree, affecting -test package

 -- Steffen Moeller <moeller@debian.org>  Mon, 12 Feb 2018 18:59:19 +0100

htslib (1.6-4) unstable; urgency=medium

  * Fix autopkgtest: Ship new files win/rand.c and win/rand.h
    in htslib-test (Closes: #866137)

 -- Graham Inggs <ginggs@debian.org>  Thu, 21 Dec 2017 15:03:36 +0000

htslib (1.6-3) unstable; urgency=medium

  * Ship a copy of cram headers in htslib-test instead of
    using symlinks (Closes: #866137)
  * Fix autopkgtest on i386 with GCC 7, see #881149

 -- Graham Inggs <ginggs@debian.org>  Wed, 20 Dec 2017 14:53:46 +0000

htslib (1.6-2) unstable; urgency=medium

  * Fix version of new symbols
  * Remove links that were provided to enable build of previous versions
    of bcftools but are not needed any more
  * Remove tabix dependency which was provided to enable build of a
    previous version of bcftools
  * Make sure no remainings of build time test will occur in test data
    package
  * Add missing override

 -- Andreas Tille <tille@debian.org>  Thu, 14 Dec 2017 15:37:03 +0100

htslib (1.6-1) experimental; urgency=medium

  * New upstream version
  * Switch to default Debian Med repository layout
  * Remove debian/patches/literal_version.patch since upstream stops
    running make to get the version number
  * Update symbols file

 -- Andreas Tille <tille@debian.org>  Mon, 11 Dec 2017 14:26:11 +0100

htslib (1.5-6) unstable; urgency=medium

  * Do not install htslib*.mk fragments
    Closes: #881360

 -- Andreas Tille <tille@debian.org>  Mon, 11 Dec 2017 13:58:23 +0100

htslib (1.5-5) unstable; urgency=medium

  [ Graham Inggs ]
  * Extend i386 fix to hurd and kfreebsd

  [ Helmut Grohne ]
  * Fix FTCBFS: Let dh_auto_configure pass --host to ./configure
    Closes: #879885

  [ Andreas Tille ]
  * Fix issues with private cram headers
     - Provide cram headers in separate package libhts-private-dev.install
       Closes: #881170
     - Deactivate fix_pkg-config.patch
       Closes: #881359
  * Standards-Version: 4.1.2

 -- Andreas Tille <tille@debian.org>  Sun, 10 Dec 2017 09:00:27 +0100

htslib (1.5-4) unstable; urgency=medium

  * Fix build on i386 (Thanks to Graham Inggs <ginggs@debian.org>)
    Closes: #881149

 -- Andreas Tille <tille@debian.org>  Mon, 20 Nov 2017 22:42:09 +0100

htslib (1.5-3) unstable; urgency=medium

  * Team upload

  [ Diane Trout ]
  * Restore libhts2.symbols and update for changes from 1.4.1 and 1.5
    versions of htslib. (Closes: #879886)

  [ Graham Inggs ]
  * Update 877670.patch as it was applied upstream

 -- Diane Trout <diane@ghic.org>  Fri, 10 Nov 2017 12:38:12 +0100

htslib (1.5-2) unstable; urgency=medium

  * Apply patch provided by Graham Inggs <ginggs@debian.org> to fix FTBFS
    on armel armhf and ppc64el of bcftools
    Closes: #877670
  * Standards-Version: 4.1.1
 -- Andreas Tille <tille@debian.org>  Wed, 08 Nov 2017 08:24:26 +0100

htslib (1.5-1) unstable; urgency=medium

  * Team upload

  [ Andreas Tille ]
  * New upstream version
  * Standards-Version: 4.0.0 (no changes needed)
  * do not parse d/changelog explicitly
  * hardening=+all
  * install htslib*.mk files that are used in bcftools

  [ Steffen Moeller ]
  * [upstream/metadata] Added reference to OMICtools

  [ Matthias Klumpp ]
  * libhts-dev: Depend on missing liblzma-dev
  * Wrap and sort

 -- Matthias Klumpp <mak@debian.org>  Thu, 03 Aug 2017 22:56:42 -0400

htslib (1.4.1-5) unstable; urgency=medium

  * Team upload
  * Dereference symlinks to fix autopkgtest (Closes: #866137)

 -- Graham Inggs <ginggs@debian.org>  Wed, 19 Jul 2017 10:37:52 +0200

htslib (1.4.1-4) unstable; urgency=medium

  * Team upload
  * Fix FTBFS on s390x and sparc64, thanks Adrian Bunk (Closes: #865010)

 -- Graham Inggs <ginggs@debian.org>  Tue, 18 Jul 2017 00:49:30 +0200

htslib (1.4.1-3) unstable; urgency=medium

  * Team upload.
  * Fix FTBFS on i386. Thanks to Adrian Bunk for the patch.
    Closes: #865012

 -- Sascha Steinbiss <satta@debian.org>  Mon, 17 Jul 2017 18:25:56 +0200

htslib (1.4.1-2) unstable; urgency=medium

  * Create symlinks only for arch=indep target when target dir exists
    Closes: #864979

 -- Andreas Tille <tille@debian.org>  Sun, 18 Jun 2017 14:19:22 +0200

htslib (1.4.1-1) unstable; urgency=medium

  * New upstream version

 -- Andreas Tille <tille@debian.org>  Sun, 18 Jun 2017 00:17:35 +0200

htslib (1.4-3) experimental; urgency=medium

  * add the cram_to_bam function to the public interface of htslib because
    it is used by code in Sambamba

 -- Andreas Tille <tille@debian.org>  Thu, 04 May 2017 10:57:31 +0200

htslib (1.4-2) experimental; urgency=medium

  * Include htsfile binary into tabix package since its used by manta
    package

 -- Andreas Tille <tille@debian.org>  Tue, 02 May 2017 15:42:11 +0200

htslib (1.4-1) experimental; urgency=medium

  * New upstream version
  * Drop autoconf from Build-Depends
  * Add libbz2-dev and liblzma-dev to Build-Depends
  * Remove binary files from test results
  * Remove symbols file
  * Change library name to match soname

 -- Andreas Tille <tille@debian.org>  Tue, 21 Mar 2017 17:44:03 +0100

htslib (1.3.2-3) experimental; urgency=medium

  * Install header files from cram dir in -dev package since these are
    used in libseqlib
  * Fix pkg-config

 -- Andreas Tille <tille@debian.org>  Fri, 10 Feb 2017 08:46:29 +0100

htslib (1.3.2-2) unstable; urgency=medium

  * Add build-essential and @builddeps@ to autopkgtest
  * debhelper 10
  * d/watch: version=4

 -- Andreas Tille <tille@debian.org>  Sat, 14 Jan 2017 19:23:52 +0100

htslib (1.3.2-1) unstable; urgency=medium

  * New upstream version

 -- Andreas Tille <tille@debian.org>  Fri, 04 Nov 2016 12:58:19 +0100

htslib (1.3.1-3) unstable; urgency=medium

  * Fix build on hurd (thanks for the patch to Svante Signell
    <svante.signell@gmail.com>)
    Closes: #836190
  * Add myself to uploaders

 -- Andreas Tille <tille@debian.org>  Thu, 01 Sep 2016 10:01:23 +0200

htslib (1.3.1-2) unstable; urgency=medium

  [ Canberk Koç ]
  * Team upload.
  * Autopktest added

  [ Andreas Tille ]
  * hardening=+bindnow

 -- Canberk Koç <canberkkoc@gmail.com>  Wed, 03 Aug 2016 04:21:17 +0300

htslib (1.3.1-1) unstable; urgency=medium

  36bf59a Merge tag '1.3.1' into debian/unstable
  559f8b4 Remove add_largefile.patch, applied upstream.
  7163afb Update symbols file. Missing _vcf_parse_format@Base and fai_read@Base.
  c2c1df3 Build-depend on libcurl4-gnutls-dev and libssl-dev.
  3b219b8 Enable libcurl.
  9101580 Conforms to the Policy version 3.9.8.

 -- Charles Plessy <plessy@debian.org>  Mon, 25 Apr 2016 22:28:11 +0900

htslib (1.3-2) unstable; urgency=medium

  * Team upload

  [ Steffen Moeller and Jon Ison ]
  * Introduction of EDAM annotation

  [ Sascha Steinbiss ]
  * Include upstream patch for large file support
  * Run configure as part of the build

 -- Sascha Steinbiss <sascha@steinbiss.name>  Mon, 08 Feb 2016 16:46:35 +0000

htslib (1.3-1) unstable; urgency=medium

  * Team upload
  * New upstream version
  * Ignore metadata files different between git and tarball

 -- Sascha Steinbiss <sascha@steinbiss.name>  Sat, 30 Jan 2016 12:16:06 +0000

htslib (1.2.1-2) unstable; urgency=medium

  * Team upload
  * Enable build on hurd-i386
    Closes: #793512
  * More verbose description vor -dev and -test package
  * Fix lintian override
  * Verified Mayhem bug report which is solved in this version
    Closes: #716376

 -- Andreas Tille <tille@debian.org>  Wed, 09 Dec 2015 17:00:47 +0100

htslib (1.2.1-1) unstable; urgency=medium

  0662716 Merge tag '1.2.1' into debian/unstable
  084f27d Install NEWS as upstream changelog.
  316fb96 Override a Lintian false positive.
  3363679 Clean test directory.
  69bf167 Corrected a typo in tabix description.

 -- Charles Plessy <plessy@debian.org>  Mon, 25 May 2015 13:35:03 +0900

htslib (1.1-1) unstable; urgency=medium

  1357fbd Merge tag '1.1' into debian/unstable
  87549cd Updated symbols file.  One symbol is missing.
  873ea9b Removed orphan paragraph in machine-readable copyright file.
  49de2b9 Allow parallel build.
  7fe3bb5 Normalise control file (VCS-Browser, Pre-Depends).
  0e5e9e6 Conforms to Policy 3.9.6.

 -- Charles Plessy <plessy@debian.org>  Wed, 24 Sep 2014 21:24:11 +0900

htslib (1.0-2) unstable; urgency=medium

  Uploaded to unstable (see previous changelog from experimental).

 -- Charles Plessy <plessy@debian.org>  Tue, 16 Sep 2014 20:27:04 +0900

htslib (1.0-1) experimental; urgency=low

  cc559b8 Merged with upstream's master branch.
  74b9d7b Build on the master branch.
  04815a7 New major version (libhts0 -> libhts1).
  98c18ca Updated symbols file.
  22fef0c Install pkgconfig file.
  420896b Override PACKAGE_VERSION to avoid tags with a slash in the name.
  79b5d4e Use the Debian package version as PACKAGE_VERSION.
  72b5c4a Finally use the 3.0 (quilt) format in single-debian-patch mode.
  d870946 Adjusted substitution variables following dpkg's warnings.
  9469458 Removed debug command accidentally introduced.
  8c7f7d4 Replace the old tabix package from the tabix source package.

 -- Charles Plessy <plessy@debian.org>  Sun, 17 Aug 2014 20:12:28 +0900

htslib (0.2.0~rc3-1) unstable; urgency=low

  * Initial release. (Closes: #729282)

 -- Charles Plessy <plessy@debian.org>  Sat, 16 Nov 2013 15:35:03 +0900