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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gatk/walkers	Secondary alignments were not handled correctly in IndelRealigner	2013-05-06 19:09:10 -04:00
utils	Added hidden mode for BQSR to force all read groups to be the same one.	2013-05-06 19:09:10 -04:00