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gatk-3.8/protected/java/src/org/broadinstitute/sting
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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 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
package-info.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00