[med-svn] samtools annotated tag 0.2.0-rc4 created (now 4e89e83)

[Charles Plessy]

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plessy pushed a change to annotated tag 0.2.0-rc4
in repository samtools.

        at  4e89e83   (tag)
   tagging  8b5a948d92797259f0174f6216e21ad33ccc313f (commit)
  replaces  0.2.0-rc3
 tagged by  John Marshall
        on  Mon Nov 18 13:00:21 2013 +0000

- Log -----------------------------------------------------------------
Test release RC4

John Marshall (3):
      Merge branch fixmate of git://github.com/mp15/samtools
      Fix typo; fixes #85.
      Merge pull request #91 from mp15/fixmate

Martin Pollard (20):
      Some initial comments whilst I think how to fix this.
      Split out syncing of mate flags
      First draft of fixed fixmates program
      Second draft of revised fixmates
      Add code to disable proper pair check.
      Polish by adding a little info to manual page, ensuring unmapped unpaired reads are treated the same as paired ones and adding details to how things work comment.
      Fix assert > to >=.
      Set the PAIRED flag once we have a pair
      Fix edge case where last read in BAM is unpaired.
      Fix compiler warning about \!
      Fix accidently inverted flag check for unmapped
      Add a few tests for fixmate
      Add GPL header template.
      Add brackets around bam_mating core unmapped check to avoid warning.
      Fix edge case where pos = 1, caused by fact bam1_t is 0 based whilst sam text format is 1 based.
      Correct flag check
      Add MQ tags when doing fixmates.
      Use STDIN_FILENO constant rather than fileno(stdin) and same for stderr in bam_mate.c.
      Port to new htslib architecture
      Make "CT" aux tag defined in bam_mate.c "ct" because it conflicts with existing defined CT tag.

Petr Danecek (14):
      mpileup: Added -x option to disable overlap detection
      Updated tests and recovered output previously disabled for debugging
      Check return status of IO calls to prevent gcc 4.6.3 warnings
      mpileup: Detect non-recoverable errors and exit with proper status
      Merge branch 'develop' of github.com:samtools/samtools into develop
      stats: Removed a too strict assert
      Merge branch 'fix' into calling
      Merge branch 'calling' into develop
      stats: Fixed off-by-one error in GCD stats which overestimated GC content by 1 part in GCD bin size
      Merge branch 'calling' into develop
      Check return status of IO calls to prevent gcc 4.6.3 warnings
      mpileup: Detect non-recoverable errors and exit with proper status
      stats: Fixed off-by-one error in GCD stats which overestimated GC content by 1 part in GCD bin size
      Merge branch 'develop' into calling

peterjc (1):
      Raise error if give @HD SO:coordinate to 'samtools fixmate'

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