Mark DePristo 7df47418d8 BQSR optimization: make RecalibrationTables thread-local, and merge results in onTraversalDone ... -- With the newer, faster BQSR, scaling was limited by the NestedIntegerArray. The solution to this is to make the entire table thread-local, so that each nct thread has its own data and doesn't have any collisions. -- Removed the previous partial solution of having a thread-local quality score table -- Added a new argument -lowMemory		2013-01-04 11:39:24 -05:00
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gatk	BQSR optimization: make RecalibrationTables thread-local, and merge results in onTraversalDone	2013-01-04 11:39:24 -05:00
utils	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
package-info.java	build system overhaul	2012-05-17 15:16:29 -04:00