Mark DePristo 0387ea8df9 Bugfix for ReadClipper with ReducedReads ... -- The previous version of the read clipping operations wouldn't modify the reduced reads counts, so hardClipToRegion would result in a read with, say, 50 bp of sequence and base qualities but 250 bp of reduced read counts. Updated the hardClip operation to handle reduce reads, and added a unit test to make sure this works properly. Also had to update GATKSAMRecord.emptyRead() to set the reduced count to new byte[0] if the template read is a reduced read -- Update md5s, where the new code recovers a TP variant with count 2 that was missed previously		2013-04-29 11:12:09 -04:00
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java	Bugfix for ReadClipper with ReducedReads	2013-04-29 11:12:09 -04:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00