htslib (1.21+ds-1) unstable; urgency=medium

  * Migrate htslib 1.21 from experimental to unstable.

 -- Étienne Mollier <emollier@debian.org>  Thu, 06 Feb 2025 21:23:41 +0100

htslib (1.21+ds-0+exp2) experimental; urgency=medium

  * d/libhts3t64.symbols: htslib_nibble2base is architecture specific.
    This symbol is an alternative function to nibble2base_default when
    SSSE3 or NEON vector instructions are available, limiting the set of
    supported architectures to a peculiar set.  Updating the symbol table
    so it matches exposed list on architectures that do not support the
    accelerated symbol.

 -- Étienne Mollier <emollier@debian.org>  Wed, 13 Nov 2024 20:47:53 +0100

htslib (1.21+ds-0+exp1) experimental; urgency=medium

  * New upstream version 1.21+ds
  * cram_to_bam_export.patch: delete: upstream exposed cram_to_bam.
    Note that cram_to_bam is an internal symbol that should not be used
    in normal situations.
  * d/patches/*: unfuzz patches.
  * d/libhts3t64.symbols: record newly introduced symbols.
  * fix_sequence_of_linked_libs.patch: normalise Last-Update.
  * d/libhts3t64.lintian-overrides: delete.
    package-name-doesnt-match-sonames was now an unused override.
  * d/htslib-test.lintian-overrides: flag false positive documentation.
  * d/libhts-dev.lintian-overrides: new.
    Hide the unstripped-static-library affecting libhts.a.  A comment in
    d/rules suggests symbols are needed by reverse dependency sambamba.

 -- Étienne Mollier <emollier@debian.org>  Tue, 12 Nov 2024 23:06:44 +0100

htslib (1.20+ds-2) unstable; urgency=medium

  * Team upload.
  * d/control: libhts-dev: Add missing dependency on libbz2-dev.
    Closes: #1086367, #1086368.

 -- Santiago Vila <sanvila@debian.org>  Thu, 31 Oct 2024 18:32:00 +0100

htslib (1.20+ds-1) unstable; urgency=medium

  * New upstream version 1.20+ds
  * d/copyright: update copyright year.
  * d/control: declare compliance to standards version 4.7.0.
  * Patch fix_float_precision: refresh.
  * testShebang.patch: unfuzz.
  * d/libhts3t64.symbols: introduce new upstream functions.

 -- Étienne Mollier <emollier@debian.org>  Wed, 29 May 2024 12:25:07 +0200

htslib (1.19+ds-1.1) unstable; urgency=medium

  * Non-maintainer upload.
  * Rename libraries for 64-bit time_t transition.  Closes: #1062344

 -- Lukas Märdian <slyon@debian.org>  Wed, 28 Feb 2024 10:41:39 +0000

htslib (1.19+ds-1) unstable; urgency=medium

  * Migrate htslib 1.19 from experimental to unstable.

 -- Étienne Mollier <emollier@debian.org>  Sat, 17 Feb 2024 11:42:52 +0100

htslib (1.19+ds-0+exp0) experimental; urgency=medium

  * New upstream version 1.19+ds
  * fix_float_precision: refresh patch.
  * fix_sequence_of_linked_libs: refresh patch.
  * trim-file-prefix.patch: refresh.
  * d/libhts3.symbols: remove a recorded symbol(!)
    bgzf_idx_amend_last was recorded by accident and is not part of the
    internals of the htslib anymore.  Reverse dependencies had no way of
    using this function by accident, as it is not part of the public API,
    and preliminary tests against reverse dependencies show no regressions
    seemingly related to the missing symbol.
  * reinject-bgzf_idx_amend_last.patch: unapplied new.
    This patch is kept handy to reintroduce missing bgzf_idx_amend_last
    symbol if need be, but it is not applied yet.

 -- Étienne Mollier <emollier@debian.org>  Fri, 15 Dec 2023 22:25:33 +0100

htslib (1.18+ds-1) unstable; urgency=medium

  * Migrate htslib 1.18 from experimental to unstable.

 -- Étienne Mollier <emollier@debian.org>  Tue, 07 Nov 2023 19:46:30 +0100

htslib (1.18+ds-0+exp1) experimental; urgency=medium

  * New upstream version 1.18+ds
  * testShebang.patch: refresh.
  * fix_float_precision: refresh patch.
  * cram_to_bam_export.patch: refresh.
  * fix_sequence_of_linked_libs.patch: refresh.
  * trim-file-prefix.patch: refresh.
  * fix-cram-external-header.patch: remove: applied upstream.
  * fix-whatis-entry.patch: remove: applied upstream.
  * debian/*.symbols*: introduce new symbols.
  * d/copyright: update upstream copyright year.

 -- Étienne Mollier <emollier@debian.org>  Wed, 23 Aug 2023 18:42:10 +0200

htslib (1.17+ds-1) unstable; urgency=medium

  * Migrate htslib to unstable.
  * d/control: declare libhts3 breaks samtools < 1.17.

 -- Étienne Mollier <emollier@debian.org>  Thu, 22 Jun 2023 22:21:42 +0200

htslib (1.17+ds-0+exp1) experimental; urgency=medium

  * New upstream version
  * Standards-Version: 4.6.2 (routine-update)
  * d/control: fix indentation in build dependencies
  * d/control: clear fields with obsolete packages
  * Patches triage:
    - no_git_version patch: forwarding not-needed
    - fPIC.patch: unfuzz
    - cram_to_bam_export.patch: unfuzz
    - fix_sequence_of_linked_libs.patch: unfuzz
    - trim-file-prefix.patch: refresh
  * fix-cram-external-header.patch: new patch.
    This fixes a FTBFS caused by a typo in the source code.
  * d/libhts3.symbols: update symbols table.
    Upstream is now tracking symbols versioning.  The change is large with
    numerous missing entries, but that is because of the "@Base" being
    replaced by the versioned "@HTSLIB_*" entries.
  * d/t/run-unit-test: copy htslib.map.
    This file is needed for one of the linking tests done during the
    autopkgtest run, otherwise it fails.
  * fix-whatis-entry.patch: new patch.
    This change fixes a bad whatis(1) entry caught by lintian.

 -- Étienne Mollier <emollier@debian.org>  Sun, 11 Jun 2023 20:10:19 +0200

htslib (1.16+ds-3) unstable; urgency=medium

  * d/rules: make sure libdir and plugindir are defined.
    Thanks to James Bonfield
  * d/libhts3.install: relocate plugins following fix at configure step.
  * d/*.install: remove dh-exec shebang.
  * d/control: remove build-dependency to dh-exec.
  * disable_plugin_loading_test.patch: remove; test is supposed to pass.
  * d/rules: do not erase LDFLAGS; fix the aforementioned test failure
    by restoring -rdynamic flag supposed to be passed to the linker.
  * d/patches/: remove unused patches.
  * trim-file-prefix.patch: add; improve reproducible build.

 -- Étienne Mollier <emollier@debian.org>  Wed, 19 Oct 2022 22:25:57 +0200

htslib (1.16+ds-2) unstable; urgency=medium

  * Team Upload.
  * Copy htslib.pc.in also to AUTOPKGTEST_TMP
  * Pass correct upstream version so as to not get the +ds
    non-sense in SOVERSIONS

 -- Nilesh Patra <nilesh@debian.org>  Sat, 01 Oct 2022 11:01:03 +0530

htslib (1.16+ds-1) unstable; urgency=medium

  * New upstream version
  * Standards-Version: 4.6.1 (routine-update)
  * Fix lintian-overrides
  * Fix build options to make sure symbols will remain in library

 -- Andreas Tille <tille@debian.org>  Fri, 30 Sep 2022 11:23:39 +0200

htslib (1.14+ds-1~exp1) experimental; urgency=medium

  * New upstream version
  * Remove constraints unnecessary since buster:
    + libhts3: Drop versioned constraint on python3-pysam in Breaks.

 -- Andreas Tille <tille@debian.org>  Tue, 07 Dec 2021 08:28:36 +0100

htslib (1.13+ds-2) unstable; urgency=medium

  * d/control: add myself to uploaders
  * d/control: libhts-dev breaks samtools (<< 1.13~)
  * d/control: refresh libhts-dev Breaks+Replaces
  * d/control: libhts-dev breaks ivar (<< 1.3.1~)

 -- Étienne Mollier <emollier@debian.org>  Fri, 27 Aug 2021 22:02:59 +0200

htslib (1.13+ds-1) unstable; urgency=medium

  [ Steffen Moeller ]
  * New upstream version
  * added libhtscodecs-dev as build-dependency
  * remove htscodecs folder from source tree (following advice
    by John Marshall - many thanks!)
  * Builds fine with autoconf > 2.71 (Closes: #978835).

  [ Andreas Tille ]
  * Standards-Version: 4.6.0 (routine-update)
  * Do not parse d/changelog (routine-update)
  * Remove constraints unnecessary since buster:
    + libhts3: Drop versioned constraint on python-pysam in Breaks.

 -- Andreas Tille <tille@debian.org>  Thu, 26 Aug 2021 18:33:04 +0200

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

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