[med-svn] samtools annotated tag 1.1 created (now 34c6691)

[Charles Plessy]

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plessy pushed a change to annotated tag 1.1
in repository samtools.

        at  34c6691   (tag)
   tagging  68ca9776ce01cfb322d5811a39f02547842621db (commit)
  replaces  1.0
 tagged by  John Marshall
        on  Fri Sep 19 16:52:34 2014 +0100

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

Christian Krause (2):
      fixes #271
      fixes #272

James Bonfield (2):
      Modified the mpileup tests to have local copies of appropriate
      Free the kstring allocated in bam_fillmd1_core in all cases

John Marshall (18):
      Merge version number bump from master branch
      No need to initialise array anyway
      Merge stats checksums
      Replace bcftools+bcf_filter.sh with new vcf-miniview
      Insulate test case from $GREP_OPTIONS
      Update expected output with symbolic "<X>" alleles
      Update QS values in expected output, and don't truncate them
      Merge minimal MD5 reference area for mpileup tests
      Merge #! fixes to misc/ scripts
      Formatting fixes for better grinding into HTML
      Recanonicalise test/test.pl whitespace -- USE -b/-w TO DIFF/BLAME
      Recanonicalise padding.c whitespace -- USE -b/-w TO DIFF/BLAME
      Merge abort/assert reduction (PR #290)
      Merge fixmate ct improvements (PR #292)
      Remove view -Q qual_scale option
      Describe compression level settings
      Use hash table to merge reference sequence headers
      Release 1.1: bug fixes

Martin O. Pollard (2):
      Reduce use of abort, remove assert(fp), pass one string to fprintf not multicall
      Fixmates ct fix

Martin Pollard (1):
      Fix fixmates for supplementary reads

Petr Danecek (3):
      stats: Compute checksum for names/seqs/quals
      Clean after fix in e3d4eee
      mpileup: conform to VCFv4.2 spec, version string should be quoted

Shane McCarthy (1):
      fix DPR annotation

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