David Roazen 991658acf4 BQSR: use more granular locking for concurrency control ... -With this change, BQSR performance scales properly by thread rather than gaining nothing from additional threads. -Benefits are seen when using either -nt (HierarchicalMicroScheduler) or -nct (NanoScheduler) -Removes high-level locks in the recalibration engines and NestedIntegerArray in favor of maximally-granular locks on and around manipulation of the leaf nodes of the NestedIntegerArray. -NestedIntegerArray now creates all interior nodes upfront rather than on the fly to avoid the need for locking during tree traversals. This uses more memory in the initial part of BQSR runs, but the BQSR would eventually converge to use this memory anyway over the course of a typical run. IMPORTANT NOTE: This does not mean it's safe to run the old BaseRecalibrator walker with multiple threads. The BaseRecalibrator walker is and will never be thread-safe, as it's a LocusWalker that uses read attributes to track state information. ONLY the newer DelocalizedBaseRecalibrator can be made thread-safe (and will hopefully be made so in my subsequent commits). This commit addresses performance, not correctness.		2012-10-24 15:22:50 -04:00
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src/org/broadinstitute/sting	BQSR: use more granular locking for concurrency control	2012-10-24 15:22:50 -04:00
test/org/broadinstitute/sting	updating HC integration test.	2012-10-24 14:08:39 -04:00