Mark DePristo 1b36db8940 Make ActiveRegionTraversal robust to excessive coverage ... -- Add a maximum per sample and overall maximum number of reads held in memory by the ART at any one time. Does this in a new TAROrderedReadCache data structure that uses a reservior downsampler to limit the total number of reads to a constant amount. This constant is set to be by default 3000 reads * nSamples to a global maximum of 1M reads, all controlled via the ActiveRegionTraversalParameters annotation. -- Added an integration test and associated excessively covered BAM excessiveCoverage.1.121484835.bam (private/testdata) that checks that the system is operating correctly. -- #resolves GSA-921		2013-04-08 15:48:19 -04:00
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DummyActiveRegionWalker.java	Working version of incremental active region traversals	2013-01-23 13:46:00 -05:00
TAROrderedReadCacheUnitTest.java	Make ActiveRegionTraversal robust to excessive coverage	2013-04-08 15:48:19 -04:00
TraverseActiveRegionsUnitTest.java	Make ActiveRegionTraversal robust to excessive coverage	2013-04-08 15:48:19 -04:00
TraverseDuplicatesUnitTest.java	Cleanup ART	2013-01-11 15:17:17 -05:00
TraverseReadsUnitTest.java	Collapse the downsampling fork in the GATK engine	2013-01-28 01:50:30 -05:00