samtools (1.9-4) unstable; urgency=medium [ Michael R. Crusoe ] * Mark samtools-test as Multi-Arch: foreign. [ Andreas Tille ] * Update debian/README.Debian, install upstream NEWS as upstream changelog, install upstream README as doc, more complete debian/NEWS.Debian Closes: #922861 * Drop reduntant information in debian/reference. It is maintained in debian/upstream/metadata now. -- Andreas Tille Thu, 21 Feb 2019 17:50:17 +0100 samtools (1.9-3) unstable; urgency=medium * Do not force sse for i386 Closes: #921315 * debhelper 12 * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target -- Andreas Tille Mon, 04 Feb 2019 08:08:28 +0100 samtools (1.9-2) unstable; urgency=medium * Team upload. * Turn on SSE for i386. Closes: #917957 * Standards-Version: 4.3.0 -- Michael R. Crusoe Thu, 03 Jan 2019 00:21:01 -0800 samtools (1.9-1) unstable; urgency=medium * New upstream version * Mention the CRAM format in the description. * Fix Perl interpreter line -- Andreas Tille Wed, 12 Sep 2018 21:43:23 +0200 samtools (1.8-1) experimental; urgency=medium * New upstream version * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 * hardening=+all * Bump versioned Build-Depends: libhts-dev (>= 1.8) -- Andreas Tille Thu, 03 May 2018 12:02:20 +0200 samtools (1.7-2) unstable; urgency=medium * Install examples (since it is used in dwgsim package and might be helpful for users in general) * debhelper 11 -- Andreas Tille Thu, 29 Mar 2018 09:55:47 +0200 samtools (1.7-1) unstable; urgency=medium * New upstream version (adapted patches, mahem patch was applied upstream) * Standards-Version: 4.1.3 * Bump versioned Build-Depends: libhts-dev (>= 1.7) -- Andreas Tille Wed, 14 Feb 2018 13:22:37 +0100 samtools (1.6-4) unstable; urgency=medium * Reduce per-thread memory limit of sort tests -- Graham Inggs Sat, 23 Dec 2017 07:03:20 +0000 samtools (1.6-3) unstable; urgency=medium * Upload to unstable -- Andreas Tille Thu, 14 Dec 2017 15:59:08 +0100 samtools (1.6-2) experimental; urgency=medium * Fix versioned Build-Depends Closes: #884269 -- Andreas Tille Wed, 13 Dec 2017 07:44:31 +0100 samtools (1.6-1) experimental; urgency=medium [ Steffen Moeller ] * debian/upstream/metadata: - added references to registries - yamllint cleanliness [ Andreas Tille ] * New upstream version * Drop literal_version.patch since upstream does not use make to obtain version number any more * Switch to default Debian Med repository layout * Standards-Version: 4.1.2 * Remove unused lintian-overrides -- Andreas Tille Mon, 11 Dec 2017 15:29:44 +0100 samtools (1.5-1) unstable; urgency=medium * New upstream version * debhelper 10 * Standards-Version: 4.0.0 (no changes needed) * Bump versioned Build-Depends: libhts-dev (>= 1.5) * Add recommends to cwl-tool and fix shebang line of cwl scripts -- Andreas Tille Fri, 04 Aug 2017 17:58:11 +0200 samtools (1.4.1-1) unstable; urgency=medium * New upstream version Closes: #865008 -- Andreas Tille Sun, 18 Jun 2017 21:11:09 +0200 samtools (1.4-2) experimental; urgency=medium * Rebuild against properly named libhts which had a soname change -- Andreas Tille Tue, 21 Mar 2017 21:42:52 +0100 samtools (1.4-1) experimental; urgency=low [ Anton Khodak ] * CWL files added [ Andreas Tille ] * New upstream version * Replaced Dominique Belhachemi by my own ID as Uploader * Bump versioned Depends: libhts-dev (>= 1.4) -- Andreas Tille Tue, 21 Mar 2017 16:24:50 +0100 samtools (1.3.1-3) unstable; urgency=medium * Team upload. * Refresh existing patches. * Fix FTBFS by including upstream patches. Closes: #840974 -- Sascha Steinbiss Mon, 24 Oct 2016 16:33:30 +0200 samtools (1.3.1-2) unstable; urgency=medium 952da10 Build-depends on htslib 1.3.1. (Closes: #822701) -- Charles Plessy Sun, 08 May 2016 21:11:12 +0900 samtools (1.3.1-1) unstable; urgency=medium 0c961b2 Merge tag '1.3.1' into debian/unstable 3666b08 Conforms with Policy version 3.9.8. -- Charles Plessy Tue, 26 Apr 2016 21:12:05 +0900 samtools (1.3-1) unstable; urgency=medium [ Charles Plessy ] 95c561d Merge tag '1.3' into debian/unstable [ Sascha Steinbiss ] * Team upload * Adapt to new build system * Use secure Vcs-Git * Patch autoconf not to use make to extract version * Clean up d/copyright * Fix spelling -- Sascha Steinbiss Fri, 05 Feb 2016 08:32:40 +0000 samtools (1.2-4) unstable; urgency=medium * Team upload * Fix synopsis * Fix Vcs-Browser * Add lintian-override to document that the language extensions are used internally * Fix spelling * Fix Mayhem issues caused by unlimited reads of gz input Closes: #716199, #716197 * Provide some more manpages -- Andreas Tille Mon, 21 Dec 2015 13:49:05 +0100 samtools (1.2-3) unstable; urgency=medium * Team upload. [19de55e] Revert "Allow all scripts to be called without language extensions" (Closes: #799698) [658179c] Revert "Remove source files not present in upstream tarball" -- Afif Elghraoui Tue, 22 Sep 2015 06:42:01 -0700 samtools (1.2-2) unstable; urgency=medium [ Afif Elghraoui ] eb56918 Add patch to fix building on i386 702d289 Remove source files not present in upstream tarball 7afd302 Allow all scripts to be called without language extensions [ Charles Plessy ] 876f680 Document the update workflow of the source package's repository. -- Charles Plessy Thu, 17 Sep 2015 20:21:15 +0900 samtools (1.2-1) unstable; urgency=medium a5f28a0 Merge tag '1.2' into debian/unstable c542e84 Build-depend on libhts-dev 1.2. 6c2d9cd Build-depend and recommend libio-pty-perl. (Needed for the regression tests.) 23e44a4 Removed fix_coverage_cap.patch, obsoleted by -d option. 1091aab Refreshed fuzzy patches. -- Charles Plessy Tue, 16 Jun 2015 06:12:12 +0900 samtools (1.1-1) unstable; urgency=medium c448d48 Merge tag '1.1' into debian/unstable d12ab1e Merge branch 'develop' into debian/unstable to solve issue with regression tests needing a pseudo-terminal. See https://github.com/samtools/samtools/issues/300 c87f8ce Add autopkg tests. 7c50b7b Removed python-wrong-path-for-interpreter.patch (issue solved upstream). -- Charles Plessy Thu, 25 Sep 2014 09:04:20 +0900 samtools (1.0-1) unstable; urgency=low [ Charles Plessy ] 54ca0c1 Merge with upstream's develop branch. 241a731 razip was removed from samtools. dc25b81 debian/watch: also track release candidates. 07aaf71 Indicate repository layout in git-buildpackage conf. file. * debian/control 8bc0fb7 Stop depending on CDBS and quilt. e613142 Drop static libbam, replaced by the dynamic libhts (Closes: #544976). b5f284c Build-depend on tabix for the regression tests, that use bgzip. 9febad6 Recommend python since samtools installs a python script in /usr/bin. 0446ed7 Conforms with Policy 3.5.6. * New package samtools-test 7293cca Create a test package for the test data. 6bd7b89 Adjust install file for two-package build. caff5f5 Clean before installing test files (this removes compiled files). * debian/rules c930cbb Use Debhelper instead of CDBS and rely on the new upstream Makefile. 845581d Adjust for dynamic linking. d859052 Indicate path to packaged bgzip. cb23517 Mimick Makefile's CPPFLAGS. aee1c6c Allow parallel building. edc09e4 Prevent Makefile from including local copy of the HTSlib. * debian/patches f73d764 d062687 Refreshed patches. 2c52f6a 61ac2c5 Forwarded patches on GitHub. b8eb378 Dropped fix_example_makefile.patch, obsolete. 66079b9 Correct path to python interpreter. 218c1c1 Modify Makefile to facilitate dynamic linking. [ Andreas Tille ] f69f412 Versioned Build-Depends libhts-dev >= 1.0 -- Charles Plessy Tue, 23 Sep 2014 09:36:27 +0900 samtools (0.1.19-1) unstable; urgency=low cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua. 2f2d5c5 debian/copyright: collapsed copyright notices from main holders. e194f9e Removed fix_float_tag.patch, corrected upstream. 9c0e543 Refreshed patches. 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch. 8d8550e example/Makefile: pass -lpthread when compiling calDepth. fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS. 6f75b48 debian/control: normalised with cme. e13bb5e debian/control: normalised VCS URLs. a1b1b00 debian/control: deleted DM-Upload-Allowed field. ddcd54e Use NEWS as upstream changelog. 81ad760 Conforms to Policy version 3.9.4. -- Charles Plessy Sat, 30 Mar 2013 17:31:47 +0900 samtools (0.1.18-4) unstable; urgency=low [Charles Plessy] * debian/copyright: Normalised with config-model * added bash completion * Build-depend on Debhelper 9 * Pass build flaggs set by dpkg-buildflags via Debhelper * Moved DOI and PubMed to the Reference namespace * Do not compress the example binary alignment file * Mention ‘SAMtools’ in libbam-dev's description [Andreas Tille] * debian/upstream: replaced BibTeX entry [Dominique Belhachemi] * added patch to fix float tag bug (upstream bug 71) -- Dominique Belhachemi Fri, 21 Dec 2012 12:09:18 -0500 samtools (0.1.18-3) unstable; urgency=low * upload 0.1.18-2 closed the wrong bug, correction: * added patch to fix segfault in mpileup (Closes: #653042) * added patch to fix coverage cap (Closes: #671524) -- Dominique Belhachemi Fri, 27 Jul 2012 11:11:41 -0400 samtools (0.1.18-2) unstable; urgency=low * added patch to fix segfault in mpileup (Closes: #544976) * added patch to fix coverage cap (Closes: #671524) -- Dominique Belhachemi Thu, 26 Jul 2012 18:30:48 -0400 samtools (0.1.18-1) unstable; urgency=low [b990d9d3] New upstream release. [d59366b9] Updated copyright statements. [aa08abe5] Compress binary packages with xz. [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch. -- Charles Plessy Tue, 06 Sep 2011 16:52:04 +0900 samtools (0.1.17-1) unstable; urgency=low * New upstream release 0.1.17 (6 July, 2011). * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages). * Patched the example makefile to not use samtools pileup, deprecated. (debian/control, debian/rules, debian/patches/series, debian/patches/no-pileup-tests.patch) -- Charles Plessy Mon, 11 Jul 2011 21:04:30 +0900 samtools (0.1.16-1) unstable; urgency=low * New upstream release, implementing SAM Spec v1.4. * Distribute sam.h and the other headers in /usr/include/samtools. Closes: #625622, #626044, LP: #690997. -- Charles Plessy Thu, 19 May 2011 13:24:25 +0900 samtools (0.1.15-1) unstable; urgency=low * New upstream release. * Incremented Standards-Version to reflect conformance with Policy 3.9.2 (debian/control, no changes needed). * debian/watch directly interrogates and downloads froms SourceForge. -- Charles Plessy Tue, 12 Apr 2011 19:44:41 +0900 samtools (0.1.14-1) unstable; urgency=low * New upstream release. -- Charles Plessy Tue, 29 Mar 2011 13:13:54 +0900 samtools (0.1.13-1) unstable; urgency=low * New upstream release: - backward incompatible with VCF/BCF generated by samtools older than r921 inclusive (0.1.12a is r862); - buildable with with ld --as-needed (Closes: #606004); - the helper tool bcf-fix.pl was removed. * Install the manual page of bcftools (debian/rules, debian/samtools.manpages). Closes: #616025. -- Charles Plessy Wed, 02 Mar 2011 13:54:34 +0900 samtools (0.1.12a-1) unstable; urgency=low * New upstream release. * Use bzip2 compression for the binary packages (debian/rules). * Incremented debhelper compatibility level to 8, in case ‘--‘ is not available in earlier versions (debian/compat, debian/control). -- Charles Plessy Fri, 03 Dec 2010 13:32:21 +0900 samtools (0.1.10-1) unstable; urgency=low * New upstream release. -- Charles Plessy Wed, 17 Nov 2010 20:32:40 +0900 samtools (0.1.9-1) unstable; urgency=low * New upstream release, and new program: bcftools. * debian/rules, debian/samtools.install: install bcftools, its manpage, and bcf-fix.pl and vcfutils.pl. * debian/samtools.examples, debian/rules: install and clean new examples. * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/control, no changes needed). * Updated and reformatted debian/copyright according to latest DEP-5 draft. -- Charles Plessy Mon, 01 Nov 2010 20:06:32 +0900 samtools (0.1.8-1) unstable; urgency=low * New upstream release. * Updated the VCS fields to the current Git repository (debian/control). * Install python scripts in usr/share/samtools, and suggest python (debian/samtools.install, debian/rules, debian/control). * Incremented Standards-Version to reflect conformance with Policy 3.9.0 (debian/control, no changes needed). * Added notes on how the package is tested (debian/README.Debian). -- Charles Plessy Wed, 14 Jul 2010 14:08:59 +0900 samtools (0.1.7a~dfsg-1) unstable; urgency=low * New upstream release: new script sam2vcf.pl, and many other changes. * Package converted to the format ‘3.0 (quilt)’ (debian/source/format). * Wrote a manual page for razip (debian/razip.1). * Better clean the example directory to make the source package buildable twice in a row (debian/rules). -- Charles Plessy Tue, 17 Nov 2009 21:38:24 +0900 samtools (0.1.6~dfsg-1) unstable; urgency=low * New upstream release. * Upstream sources repackaged to remove the win32 directory: - The removal was done with git-import-orig in a parallel Git repository, and the corresponding debian/gbp.conf file was added to this package. - Mangled the ~dfsg string of the Debian version in debian/watch. - Added a debian/README.source file and explanations in debian/copyright. -- Charles Plessy Mon, 14 Sep 2009 21:58:36 +0900 samtools (0.1.5c-2) unstable; urgency=low * Rebuilt with -fPIC (debian/rules, README.Debian). * Small corrections to the description from upstream (debian/changelog). * Incremented Standards-Version to reflect conformance with Policy 3.8.3 (no changes needed). -- Charles Plessy Thu, 03 Sep 2009 19:29:40 +0900 samtools (0.1.5c-1) unstable; urgency=low * Initial release (Closes: #540453) -- Charles Plessy Sun, 16 Aug 2009 14:38:20 +0900