Eric Banks d242f1bba3 Secondary alignments were not handled correctly in IndelRealigner ... * This is emerging now because BWA-MEM produces lots of reads that are not primary alignments * The ConstrainedMateFixingManager class used by IndelRealigner was mis-adjusting SAM flags because it was getting confused by these secondary alignments * Added unit test to cover this case		2013-05-06 19:09:10 -04:00
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java	Secondary alignments were not handled correctly in IndelRealigner	2013-05-06 19:09:10 -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