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Eric Banks 573ed07ad0 Fixed reported bug in BQSR for RNA seq alignments with Ns. 
* ClippingOp updated to incorporate Ns in the hard clips.
  * ReadUtils.getReadCoordinateForReferenceCoordinate() updated to account for Ns.
  * Added test that covers the BQSR case we saw.
  * Created GSA-856 (for Mauricio) to add lots of tests to ReadUtils.
    * It will require refactoring code and not in the scope of what I was willing to do to fix this.
 		2013-03-14 11:26:52 -04:00
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config Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
src Fixed reported bug in BQSR for RNA seq alignments with Ns. 2013-03-14 11:26:52 -04:00
test Fixed reported bug in BQSR for RNA seq alignments with Ns. 2013-03-14 11:26:52 -04:00