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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R	Fixed spelling error in BQSR.R	2012-08-13 10:01:33 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Removing parallelism bottleneck in the GATK	2012-08-15 21:13:15 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Added setupRetry() to modify jobs when Queue is run with '-retry' and jobs are about to restart after an error.	2012-08-13 15:43:05 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00