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Mark DePristo e1293f0ef2 GSA-507: Thread monitoring refactored so it can work without a thread factory 
-- Old version StateMonitoringThreadFactory refactored into base class ThreadEfficiencyMonitor and subclass EfficiencyMonitoringThreadFactory.
-- Base class is used by LinearMicroScheduler to monitor performance of GATK in single threaded mode
-- MicroScheduler now handles management of the efficiency monitor.  Includes master thread in monitor, meaning that reduce is now included for both schedulers
 		2012-08-22 16:48:01 -04:00
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R Fix for missing formatter in R 2.15 2012-08-17 11:49:02 -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
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java GSA-507: Thread monitoring refactored so it can work without a thread factory 2012-08-22 16:48:01 -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 Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters) 2012-06-07 16:56:32 -04:00
scala Complete GSA-497: Let Queue write out runInfo on the fly, after each job group finishes running 2012-08-21 14:44:18 -04:00
testdata Reverting move of BQSR tests to public, as per DR's email 2012-07-19 10:02:05 -04:00