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  1. Aug 06, 2010
  2. Aug 05, 2010
  3. Aug 04, 2010
  4. Jul 26, 2010
  5. Jul 23, 2010
  6. Jul 22, 2010
  7. Jul 21, 2010
  8. Jul 18, 2010
  9. Jul 17, 2010
  10. Jul 15, 2010
  11. Jul 06, 2010
  12. Jul 05, 2010
  13. Jul 04, 2010
    • Aaron's avatar
      Fixed bug in groupBy and added logic to enforce that strings are numeric when... · 7f11baac
      Aaron authored
      Fixed bug in groupBy and added logic to enforce that strings are numeric when asking for nueric ops.
      7f11baac
    • Aaron's avatar
      Large commit. · 3cba5c6c
      Aaron authored
      	A. Fixed massive bug in parseBedLine that disallowed BED features with start = 0.  Bad news.
      	1. Moved ToString to lineFileUtilities
      	2. Added tabFile class.  Works with gzip as well.
      	3. Changed groupBy to use the new TabFile class.
      	4. Added new collapse feature to groupBy.
      3cba5c6c
    • Aaron's avatar
    • Aaron's avatar
      Fixed logic relating to "split" coverage. · 9fe56c08
      Aaron authored
      	1. Fixed bug in BamAncillary::getBamBlocks where the switch statement was misbehaving.  Changed to if/else
      	2. Added countSplitHits to bedFile class to proper count coverage from "blocked" alignments. Previously, coverage
                 was counted separately for __each__ block yet what we actually want is the base coverage to be counted for each block,
                 but we only want the blocks to be treated as __one__ alignment or feature.
      	3. Updated coverageBed to use getBamBlocks.
      9fe56c08
  14. Jul 01, 2010
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