Mark DePristo f277d7c09e Removing parallelism bottleneck in the GATK ... -- GenomeLocParser cache was a major performance bottleneck in parallel GATK performance. With 10 thread > 50% of each thread's time was spent blocking on the MasterSequencingDictionary object. Made this a thread local variable. -- Now we can run the GATK with 48 threads efficiently on GSA4! -- Running -nt 1 => 75 minutes (didn't let is run all of the way through so likely would take longer) -- Running -nt 24 => 3.81 minutes		2012-08-15 21:13:15 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Removing parallelism bottleneck in the GATK	2012-08-15 21:13:15 -04:00
test	In AlleleCount stratification, check to make sure the AC (or MLEAC) is valid (i.e. not higher than number of chromosomes) and throw a User Error if it isn't. Added a test for bad AC.	2012-08-14 15:02:30 -04:00