htslib (1.19+ds-1) unstable; urgency=medium * Migrate htslib 1.19 from experimental to unstable. -- Étienne Mollier 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Mon, 05 Oct 2020 09:30:04 +0200 htslib (1.11-1) unstable; urgency=medium * New upstream version -- Andreas Tille 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 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 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 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 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 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 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 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 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 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 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 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 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 Wed, 16 Jan 2019 00:27:21 -0800 htslib (1.9-10~0libdeflate) experimental; urgency=medium * Try libdeflate again. -- Michael R. Crusoe 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 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 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 Mon, 31 Dec 2018 07:08:13 -0800 htslib (1.9-7) unstable; urgency=medium * Bring i386 build enhancements to unstable. -- Michael R. Crusoe 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 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 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 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 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 ) Closes: #911492 -- Andreas Tille Sun, 02 Dec 2018 07:54:46 +0100 htslib (1.9-3) unstable; urgency=medium * debian/control: drop *i386. Closes: #905438. -- Michael R. Crusoe 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 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 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 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 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 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 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 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 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 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 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 Sun, 10 Dec 2017 09:00:27 +0100 htslib (1.5-4) unstable; urgency=medium * Fix build on i386 (Thanks to Graham Inggs ) Closes: #881149 -- Andreas Tille 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 Fri, 10 Nov 2017 12:38:12 +0100 htslib (1.5-2) unstable; urgency=medium * Apply patch provided by Graham Inggs to fix FTBFS on armel armhf and ppc64el of bcftools Closes: #877670 * Standards-Version: 4.1.1 -- Andreas Tille 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 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 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 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 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 Sun, 18 Jun 2017 14:19:22 +0200 htslib (1.4.1-1) unstable; urgency=medium * New upstream version -- Andreas Tille 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 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 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 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 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 Sat, 14 Jan 2017 19:23:52 +0100 htslib (1.3.2-1) unstable; urgency=medium * New upstream version -- Andreas Tille 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 ) Closes: #836190 * Add myself to uploaders -- Andreas Tille 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 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 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 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 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 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 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 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 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 Sun, 17 Aug 2014 20:12:28 +0900 htslib (0.2.0~rc3-1) unstable; urgency=low * Initial release. (Closes: #729282) -- Charles Plessy Sat, 16 Nov 2013 15:35:03 +0900