[med-svn] samtools annotated tag 0.1.10 created (now 8b2a4fa)

[Charles Plessy]

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plessy pushed a change to annotated tag 0.1.10
in repository samtools.

        at  8b2a4fa   (tag)
   tagging  624c76e0c2b7f98b0fdf734345a61e3019e68fd3 (commit)
  replaces  0.1.9
 tagged by  On behalf of Heng Li
        on  Wed Nov 17 04:20:01 2010 +0000

- Log -----------------------------------------------------------------
Samtools 0.1.10, including ChangeLog.old and win32/lib*.a files
that were missing from the canonical release tarball, but without
the samtools.txt file (generated from samtools.1) that is found
in the tarball.

Heng Li (45):
      acknowledge Petr and John who have greatly contributed to the project.
      Optionally output "DP", the individual read depth
      * samtools-0.1.9-1 (r786)
      * samtools-0.1.9-2 (r787)
      Separate kaln and kprobaln as I am preparing further changes. At
      fixed a minor problem in the example coming with kprobaln.c
      for backup. no effective changes
      * this revision is UNSTABLE
      Revert to r790. The recent changes are not good...
      prepare for the indel caller. It is not ready yet.
      fixed a few bugs in the indel caller. Probably there are more.
      indel calling is apparently working, but more information needs to be collected
      * samtools-0.1.9-2 (r797)
      Incorporate patches by Marcel Martin for read counting.
      fixed a silly bug in the indel caller
      fixed another silly bug in mpileup's indel caller
      * samtools-0.1.9-4 (r801)
      * samtools-0.1.9-5 (r802)
      * samtools-0.1.9-6 (r803)
      * samtools-0.1.9-7 (r804)
      added a double-hit filter to avoid overestimated indel likelihood
      bcftools: compute equal-tail (Bayesian) credible interval
      * samtools-0.1.9-8 (r807)
      minor change to makefile
      * samtools-0.1.9-8 (r809)
      * do not use reads containing too many mismatches for indel calling
      use zlib for direct reading when BCF_LITE is in use
      fixed a typo
      * prepare to replace kaln with kprobaln in realignment
      * samtools-0.1.9-9 (r810)
      effectively revert to the viterbi version. The forward realignment gives too many false positives.
      * samtools-0.1.9-10 (r816)
      * samtools-0.1.19-11 (r817)
      * samtools-r818
      * samtools-0.1.9-13 (r819)
      * samtools-0.1.9-14 (r820)
      * samtools-0.1.9-15 (r821)
      * samtools-0.1.9-16 (r822)
      * samtools-0.1.9-r823
      * samtools-0.1.9-17 (r824)
      * samtools-0.1.9-18 (r825)
      remove ZQ if both BQ and ZQ are present
      bcftools: allow to skip indels
      update version information: samtools-0.1.9-20 (r828)
      Release samtools-0.1.10 (r829)

Petr Danecek (1):
      Added -b option: read file names from a file

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No new revisions were added by this update.

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