[med-svn] samtools branch master updated (68ca977 -> 255f97d)

[Charles Plessy]

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

plessy pushed a change to branch master
in repository samtools.

      from  68ca977   Release 1.1: bug fixes
      adds  db22ee9   Merge version number bump from master branch
      adds  b7c4b4d   Ensure usage tests have a terminal on stdin
       new  281bf0a   Recanonicalise regression.sh whitespace -- USE -b/-w TO DIFF/BLAME
       new  9c4099f   Set output file threading only if there is an output file
       new  29395a5   Fixed a buffer overflow when dealing with cigar strings ending with a deletion.
       new  089ecbe   Improved fix to mpileup. The previous one just skipped bases where we have no quality. This still includes them in the pileup, but with 0 qual instead.
       new  418fc0c   Also fix buffer overrun on data where the sequence is "*".
       new  2fac99b   Fixed up test data, now that it correctly outputs "n" instead.
       new  056ae75   Merge pull request #306 from jkbonfield/mpileup-fix
       new  59c56f0   Man page formatting fixes
       new  5ac61a2   Write failure messages to stderr
       new  6f1c154   Maintain HEAP_EMPTY invariant when an input is empty
       new  d2e8d7a   Avoid using htsFile is_foo bits directly
       new  4580150   Reflect changes in htslib API
       new  01465e8   Fix typo in 'samtools flagstats' output
       new  6c17071   Added a test for specifying the reference via samtools -T.  This appeared to work in our previous tests, but did not due to the code sneakily reverting to the @SQ UR: field instead.
       new  c02491f   Merge origin/develop, prefering avoiding using htsFile internals
       new  4a2320a   Avoid "my" variable redeclaration [minor]
       new  a25229a   Prevent warnings when compiling on a 32-bit host [minor]
       new  dc1f438   stats: Calculate mismatches per cycle for unclipped length
       new  6b249e2   Merge branch 'develop' of github.com:samtools/samtools into develop
       new  c61d8d1   Merge origin/develop into develop
       new  bca67a9   Convert bam2bcf_indel.c to use the htslib API directly
       new  9e3bbcf   Update comment documentation for bam_mate
       new  19c9f67   Remove unused kaln.c, kaln.h global aligner
       new  29b0367   Replace cryptic 'minQLen' with real description
       new  8dd3761   Use bam_init1/bam_destroy1 instead of creating/destroying by hand
       new  3fdca5b   Make samtools merge work with SAM input files
       new  5d6a1e3   Avoid crashing on unopenable files [minor]
       new  7f47a7c   Parse mpileup -r region against the right file's headers
       new  f3f3d6d   Large chromosome test case now passes
       new  c06f698   Add a few comments to pileup and errmod code, move some existing ones to slightly better positions.
       new  311926c   Fix typo.
       new  5c49bf9   Fixed samtools flagstat to use the samFile (htsFile) API instead of bamFile.  This means it can now work on sam, bam and cram formats instead of only bam.
       new  2a40f2e   Switch from hts_close to sam_close, for consistency (they're the same thing underneath).
       new  2bcfffd   Added various hts_set_opt calls to set the CRAM_OPT_REQUIRED_FIELDS and CRAM_OPT_DECODE_MD options to avoid doing unnecessary decoding work.
       new  a513827   Merge pull request #299 from jkbonfield/cram3
       new  581e707   bamtk.c requires only hts_version(), not <bam.h>
       new  446aae0   Happy New Year
       new  e2ce81d   Added checks to sam_hdr_write() return value.
       new  c5df8be   Added 'insert size' to the head of the IS section
       new  0cc7b47   Merge pull request #342 from nathanhaigh/develop
       new  8f50332   Documentation: Updated REF_CACHE location details.
       new  255f97d   Release 1.2: various bug fixes

The 42 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.


Summary of changes:
 INSTALL                          |   2 +-
 Makefile                         |  11 +-
 NEWS                             |  16 ++
 README                           |  23 ++
 bam.h                            |   2 +-
 bam2bcf_indel.c                  |  40 ++--
 bam2depth.c                      |  16 +-
 bam_mate.c                       |   3 +-
 bam_md.c                         |   1 -
 bam_plcmd.c                      |  45 +++-
 bam_sort.c                       |  61 +++--
 bam_stat.c                       |  40 +++-
 bamtk.c                          |   6 +-
 errmod.c                         |   7 +-
 kaln.c                           | 486 ---------------------------------------
 kaln.h                           |  67 ------
 misc/ace2sam.c                   |   2 +-
 misc/plot-bamstats               |   2 +-
 misc/seq_cache_populate.pl       |   5 +
 padding.c                        |   2 +-
 sam.c                            |   8 +-
 sam.h                            |   3 +-
 sam_view.c                       |  27 ++-
 samtools.1                       |  36 +--
 stats.c                          |  21 +-
 test/merge/test_rtrans_build.c   |   4 +-
 test/merge/test_trans_tbl_init.c |   2 +-
 test/mpileup/expected/9.out      |  20 +-
 test/mpileup/regression.sh       | 125 +++++-----
 test/stat/1.stats.expected       |   2 +-
 test/stat/2.stats.expected       |   2 +-
 test/stat/3.stats.expected       |   2 +-
 test/stat/4.stats.expected       |   2 +-
 test/stat/5.stats.expected       |   2 +-
 test/stat/6.stats.expected       |   2 +-
 test/test.pl                     |  59 ++++-
 36 files changed, 390 insertions(+), 764 deletions(-)
 delete mode 100644 kaln.c
 delete mode 100644 kaln.h

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