Mauricio Carneiro a17cd54b68 Co-Reduction implementation in ReduceReads ... ReduceReads now co-reduces bams if they're passed in toghether with multiple -I. Co-reduction forces every variant region in one sample to be a variant region in all samples. Also: * Added integrationtest for co-reduction * Fixed bug with new no-recalculation implementation of the marksites object where the last object wasn't being removed after finalizing a variant region (updated MD5's accordingly) DEV-200 #resolve #time 8m		2012-11-14 10:33:21 -05:00
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org/broadinstitute/sting	Co-Reduction implementation in ReduceReads	2012-11-14 10:33:21 -05:00