Mark DePristo 2267b722b2 Proper error handling in NanoScheduler ... -- Renamed TraversalErrorManager to the more general MultiThreadedErrorTracker -- ErrorTracker is now used throughout the NanoScheduler. In order to properly handle errors, the work previously done by main thread (submit jobs, block on reduce) is now handled in a separate thread. The main thread simply wakes up peroidically and checks whether the reduce result is available or if an error has occurred, and handles each appropriately. -- EngineFeaturesIntegrationTest checks that -nt and -nct properly throw errors in Walkers -- Added NanoSchedulerUnitTest for input errors -- ThreadEfficiencyMonitoring is now disabled by default, and can be enabled with a GATK command line option. This is because the monitoring doesn't differentiate between threads that are supposed to do work, and those that are supposed to wait, and therefore gives misleading results. -- Build.xml no longer copies the unittest results verbosely		2012-09-19 17:03:13 -04:00
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sting	Proper error handling in NanoScheduler	2012-09-19 17:03:13 -04:00