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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/sam
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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
..
AlignmentUtilsUnitTest.java Expanded functionality for writing BAMs from HaplotypeCaller 2013-03-03 12:07:29 -05:00
ArtificialBAMBuilderUnitTest.java Last manual license update (hopefully) 2013-01-18 16:13:07 -05:00
ArtificialPatternedSAMIteratorUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArtificialSAMFileWriterUnitTest.java PrintReads writes a header when used with -BQSR 2013-02-14 22:19:14 -05:00
ArtificialSAMQueryIteratorUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArtificialSAMUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArtificialSingleSampleReadStreamUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GATKSAMRecordUnitTest.java New GATKSAMRecord concept of a strandless read, update to FS 2013-03-13 11:16:36 -04:00
MisencodedBaseQualityUnitTest.java Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest 2013-02-27 04:45:53 -05:00
ReadUtilsUnitTest.java Fixed reported bug in BQSR for RNA seq alignments with Ns. 2013-03-14 11:26:52 -04:00