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