[med-svn] samtools annotated tag 1.2 created (now 6af451d)

[Charles Plessy]

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plessy pushed a change to annotated tag 1.2
in repository samtools.

        at  6af451d   (tag)
   tagging  255f97daffd3a27d7b063e991a993f47ad6186cf (commit)
  replaces  1.1
 tagged by  John Marshall
        on  Mon Feb 2 15:20:56 2015 +0000

- Log -----------------------------------------------------------------
Bug fix release

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 (22):
      Merge version number bump from master branch
      Ensure usage tests have a terminal on stdin
      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

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