[med-svn] samtools annotated tag 0.2.0-rc6 created (now dafa88b)

[Charles Plessy]

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plessy pushed a change to annotated tag 0.2.0-rc6
in repository samtools.

        at  dafa88b   (tag)
   tagging  c82cbaddd406651e5f5ad05ac49ba58e69ac7b0c (commit)
  replaces  0.2.0-rc5
 tagged by  John Marshall
        on  Thu Feb 13 17:30:59 2014 +0000

- Log -----------------------------------------------------------------
Test release RC6

Christian Brueffer (1):
      Fix typos in the manpage.

John Marshall (13):
      Rearrange (so tags can see main_depth()) [minor]
      Remove incorrect parameter check
      Fail when tests fail
      Usage message tweaks to satisfy test/test.pl's test_usage()
      Implement view & bam2fq directly against the htslib API
      Use new sam_itr_*() htslib API for BAM/CRAM iterators
      [bedcov] Use the htslib API directly, now works with BAM or CRAM files
      Use htslib's bam_endpos() instead of copied old bam_calend() code
      Merge pull request #118, fixing man page typos
      Merge pull request #141 from sb10/develop
      Merge pull request #109 from aux_tag_strip of github.com/mp15/samtools
      Merge pull request #106, properly-paired flag statistics
      Shut up, clang!

Joshua Randall (3):
      Fixed GCC section so that read cycle column begins with 1 instead of 0.
      Adds tests for usage message for samtools and all subcommands
      Modifies test.pl so that it exits with non-zero status if any tests fail.

Martin Pollard (4):
      Add properly paired to stats and correct definition in flagstat
      Replace bam2fq numbers with existing constants
      Remove global variables from samtools view
      Add ability to strip aux tags to samtools view

Petr Danecek (16):
      mpileup: Allow up to five alleles (N,A,C,G,T)
      New "flags" command plus moved filtering from htslib/pileup to BAM reading callbacks
      On behalf of Peter Chines, test that filter mask replaces (not just adds to) default mask
      mpileup: Disabled CDF version of MWU annotations and made it optional at compile time
      Merge branch 'develop' into calling
      Merge branch 'calling' into develop
      plot-bamstats: Skip generation of empty GCD graphs
      stats: Fix of mismmatch-per-cycle calculation in presence of hard-clipped reads
      Moved khash_utils.h into htslib
      Updated the khash_utils.h dependency
      stats: realloc buffers in MPC calculation if necessary, unclipped length can be bigger seq_len
      mpileup: Removed bcf_hdr_fmt_text() which is no longer necessary
      Updated test
      flags: Fixed a typo
      mpileup: -q now takes effect also with -C
      mpileup: Apply -Q switch also to MQ output

Sendu Bala (1):
      fixed spelling mistake

Shane McCarthy (1):
      samtools flags: add documentation. print out decimal representation in addition to hexadecimal and string representation

pd3 (2):
      Merge pull request #95 from wtsi-hgi/develop
      Merge pull request #121 from sm15/feature/bam_flags_docs

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