Mauricio Carneiro ec475a46b1 Fixing @PG tag uniqueness issue ... The Problem: ------------ the SAM spec does not allow multiple @PG tags with the same id. Our @PG tag writing routines were allowing that to happen with the boolean parameter "keep_all_pg_records". How this fixes it: ------------------ This commit removes that option from all the utility functions and cleans up the code around the classes that used these methods off-spec. Summarized changes: ------------------- * Remove keep_all_pg_records option from setupWriter utility methos in Util * Update all walkers to now replace the last @PG tag of the same walker (if it already exists) * Cleanup NWaySamFileWriter now that it doesn't need to keep track of the keep_all_pg_records variable * Simplify the multiple implementations to setupWriter Bamboo: ------- http://gsabamboo.broadinstitute.org/browse/GSAUNSTABLE-PARALLEL31 Issue Tracker: -------------- [fixes 47100885]		2013-03-30 20:31:33 -04:00
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src/org/broadinstitute/sting	Fixing @PG tag uniqueness issue	2013-03-30 20:31:33 -04:00
test/org/broadinstitute/sting	MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods	2013-03-29 14:52:10 -04:00