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Commits on Oct 10, 2012
Commits on Sep 12, 2012
  1. Merge remote branch 'remotes/pd3/master'

    Conflicts:
    	misc/bamcheck.c
    pd3 committed Sep 12, 2012
Commits on Sep 5, 2012
Commits on Sep 4, 2012
  1. New --GC-depth option to bamcheck. Take into account not so frequent …

    …CIGAR codes. Fix in realloc_buffers. Prevent segfault with long command line options; Set xrange correctly in plot-bamcheck coverage.gp
    pd3 committed Sep 4, 2012
Commits on Aug 21, 2012
  1. Merge pull request #14 from peterjc/depad3

    Update MPOS/PNEXT during 'samtools depad'
    lh3 committed Aug 21, 2012
Commits on Aug 17, 2012
Commits on Aug 3, 2012
Commits on Aug 2, 2012
  1. Use int64_t to prevent count overflow in view -c; on behalf of Joshua…

    … Randall: Set y2range in quals2.png plot
    pd3 committed Aug 2, 2012
Commits on Jul 18, 2012
Commits on Jul 5, 2012
Commits on Jul 3, 2012
  1. Bug fixes

    pd3 committed Jul 3, 2012
Commits on Jul 2, 2012
  1. Alternative model for multiallelic and rare-variant calling. Proof-of…

    …-principle implementation.
    pd3 committed Jul 2, 2012
Commits on Jun 27, 2012
  1. New -p switch for increased sensititivy of indel-calling. Here -m and…

    … -F are used per-sample which enables to detect rare indels in low-coverage bams. Experimental.
    pd3 committed Jun 27, 2012
Commits on Jun 21, 2012
Commits on Jun 19, 2012
  1. Merge pull request #11 from peterjc/depad2

    Depad2
    Heng Li committed Jun 19, 2012
  2. Update @SQ lines during 'samtools depad'

    Note does not (yet) preserve additional @SQ line tags (e.g. AS, SP, UR).
    committed Jun 19, 2012
  3. Wording of error messages

    committed May 14, 2012