Mark DePristo 251983b8fb Add GATK-wide command line argument to control the maximum runtime allowed for the GATK ... -- Providing this optional argument -maxRuntime (in -maxRuntimeUnits units) causes the GATK to exit gracefully when the max. runtime has been exceeded. By cleanly I mean that the engine simply stops at the next available cycle in the walker as through the end of processing had been reached. This means that all output files are closed properly, etc. -- Emits an info message that looks like "INFO 10:36:52,723 MicroScheduler - Aborting execution (cleanly) because the runtime has exceeded the requested maximum 10.0000 s". Otherwise there's currently no way to differentiate a truly completed run from a timelimit exceeded run, which may be a useful thing for a future update -- Resolves GSA-630 / GATK max runtime to deal with bad LSA calling? -- Added new JIRA entry for Ami to restart chr1 macarthur with this argument set to -maxRuntime 1 -maxRuntimeUnits DAYS to see if we can do all of chr1 in one weekend.		2012-10-26 13:18:34 -04:00
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datasources	ExperimentalReadShardBalancerUnitTest was being skipped; fixed	2012-09-22 01:56:39 -04:00
downsampling	Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"	2012-09-10 15:52:39 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Updated and more thorough version of the BadCigar read filter	2012-08-17 17:05:27 -04:00
iterators	Experimental, downsampler-friendly read shard balancer	2012-09-21 22:17:58 -04:00
refdata	Part I of GSA-462: Consistent RODBinding access across Ref and Read trackers	2012-08-30 10:15:10 -04:00
report	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
samples	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
traversals	Retiring TraverseReads and TraverseLoci after testing confirms nano scheduler version in single threaded version is fine	2012-10-22 16:55:06 -04:00
walkers	Fix UG parallelization test	2012-10-26 12:10:44 -04:00
CommandLineGATKUnitTest.java	Adding Unit Tests to cover the exception catching for Picard errors: because we are using String matching, we want to ensure that we know if/when the exception text changes underneath us.	2012-07-18 21:48:58 -04:00
EngineFeaturesIntegrationTest.java	Proper error handling in NanoScheduler	2012-09-19 17:03:13 -04:00
GenomeAnalysisEngineUnitTest.java	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
MaxRuntimeIntegrationTest.java	Add GATK-wide command line argument to control the maximum runtime allowed for the GATK	2012-10-26 13:18:34 -04:00
WalkerManagerUnitTest.java	Fixing walker unit test with the new naming convention	2012-07-20 17:50:29 -04:00