Mauricio Carneiro 2c0bf89961 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		2012-11-06 13:49:07 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Co-Reduction implementation in ReduceReads	2012-11-06 13:49:07 -05:00
test	Fixing md5s to reflect the new HapMap file	2012-10-30 14:27:10 -04:00