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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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
gatk	Forgot to update 2 integration test md5's (in this cases, changes are legit because of the code revamp of AD, it's simpler if AD is not output when a site is not variant, as genotype DP conveys the same information)	2012-08-22 15:53:33 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	GSA-507: Thread monitoring refactored so it can work without a thread factory	2012-08-22 16:48:01 -04:00
BaseTest.java	Extensive unit tests, contacts, and documentation for RecalDatum	2012-07-31 08:11:03 -04:00
MD5DB.java	Finalizing BCF2 mark III commit	2012-06-21 15:16:27 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	On the way to really sorting out HMS error handling	2012-07-25 22:11:10 -04:00