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 <plessy@debian.org>  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 <domibel@debian.org>  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 <domibel@debian.org>  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 <domibel@debian.org>  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 <plessy@debian.org>  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 <plessy@debian.org>  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 <plessy@debian.org>  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 <plessy@debian.org>  Tue, 12 Apr 2011 19:44:41 +0900

samtools (0.1.14-1) unstable; urgency=low

  * New upstream release.

 -- Charles Plessy <plessy@debian.org>  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 <plessy@debian.org>  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 <plessy@debian.org>  Fri, 03 Dec 2010 13:32:21 +0900

samtools (0.1.10-1) unstable; urgency=low

  * New upstream release.

 -- Charles Plessy <plessy@debian.org>  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 <plessy@debian.org>  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 <plessy@debian.org>  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 <plessy@debian.org>  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 <plessy@debian.org>  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 <plessy@debian.org>  Thu, 03 Sep 2009 19:29:40 +0900

samtools (0.1.5c-1) unstable; urgency=low

  * Initial release (Closes: #540453)

 -- Charles Plessy <plessy@debian.org>  Sun, 16 Aug 2009 14:38:20 +0900
