[med-svn] samtools annotated tag debian/1.2-1 created (now 4bce941)

[Charles Plessy]

This is an automated email from the git hooks/post-receive script.

plessy pushed a change to annotated tag debian/1.2-1
in repository samtools.

        at  4bce941   (tag)
   tagging  e4c31091a774ee5b44f5b1d5f6c5e6b180a09796 (commit)
  replaces  debian/1.1-1
 tagged by  Charles Plessy
        on  Tue Jun 16 06:59:04 2015 +0900

- Log -----------------------------------------------------------------
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 <plessy at debian.org>  Tue, 16 Jun 2015 06:12:12 +0900
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1
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=WmQ0
-----END PGP SIGNATURE-----

Charles Plessy (13):
      Build-depend and recommend libio-pty-perl for the regression tests.
      Current changelog.
      Make autopkg test depend on tabix.
      Merge tag '1.2' into debian/unstable
      New upstream release ; no new copyright notice nor license term.
      Corrected syntax.
      Removed fix_coverage_cap.patch, obsoleted by -d option.
      Refreshed fuzzy patches.
      Build-depend on libhts-dev 1.2.
      Current changelog.
      Revert last commit, that included patched files by mistake.
      Current changelog.
      samtools (1.2-1) unstable; urgency=medium

Gianluca Della Vedova (1):
      Fix typo.

James Bonfield (11):
      Fixed samtools flagstat to use the samFile (htsFile) API instead of
      Switch from hts_close to sam_close, for consistency (they're the same
      Fixed a buffer overflow when dealing with cigar strings ending with a
      Improved fix to mpileup. The previous one just skipped bases where we
      Also fix buffer overrun on data where the sequence is "*".
      Fixed up test data, now that it correctly outputs "n" instead.
      Added a test for specifying the reference via samtools -T.  This
      Added various hts_set_opt calls to set the CRAM_OPT_REQUIRED_FIELDS
      Merge pull request #299 from jkbonfield/cram3
      Added checks to sam_hdr_write() return value.
      Documentation: Updated REF_CACHE location details.

John Marshall (20):
      Recanonicalise regression.sh whitespace -- USE -b/-w TO DIFF/BLAME
      Set output file threading only if there is an output file
      Man page formatting fixes
      Write failure messages to stderr
      Maintain HEAP_EMPTY invariant when an input is empty
      Avoid using htsFile is_foo bits directly
      Merge origin/develop, prefering avoiding using htsFile internals
      Avoid "my" variable redeclaration [minor]
      Prevent warnings when compiling on a 32-bit host [minor]
      Merge origin/develop into develop
      Convert bam2bcf_indel.c to use the htslib API directly
      Remove unused kaln.c, kaln.h global aligner
      Use bam_init1/bam_destroy1 instead of creating/destroying by hand
      Make samtools merge work with SAM input files
      Avoid crashing on unopenable files [minor]
      Parse mpileup -r region against the right file's headers
      Large chromosome test case now passes
      bamtk.c requires only hts_version(), not <bam.h>
      Happy New Year
      Release 1.2: various bug fixes

Martin Pollard (2):
      Update comment documentation for bam_mate
      Add a few comments to pileup and errmod code, move some existing ones to slightly better positions.

Nathan S. Watson-Haigh (1):
      Added 'insert size' to the head of the IS section

Peter Cock (1):
      Fix typo in 'samtools flagstats' output

Petr Danecek (3):
      Reflect changes in htslib API
      stats: Calculate mismatches per cycle for unclipped length
      Merge branch 'develop' of github.com:samtools/samtools into develop

pd3 (2):
      Merge pull request #306 from jkbonfield/mpileup-fix
      Merge pull request #342 from nathanhaigh/develop

peterjc (1):
      Replace cryptic 'minQLen' with real description

-----------------------------------------------------------------------

This annotated tag includes the following new commits:

       new  d2e84d5   Revert last commit, that included patched files by mistake.
       new  affb220   Current changelog.
       new  e4c3109   samtools (1.2-1) unstable; urgency=medium

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git