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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datasources	Remove auto-creation of fai/dict files for fasta references	2013-04-02 18:34:08 -04:00
downsampling	Add size() method to Downsampler interface	2013-04-08 15:48:13 -04:00
executive	…
filters	…
iterators	…
refdata	…
report	…
samples	…
traversals	Make ActiveRegionTraversal robust to excessive coverage	2013-04-08 15:48:19 -04:00
walkers	Refactored the het (polyploid) consensus creation in ReduceReads.	2013-03-25 09:34:54 -04:00
CommandLineGATKUnitTest.java	…
EngineFeaturesIntegrationTest.java	…
GenomeAnalysisEngineUnitTest.java	…
MaxRuntimeIntegrationTest.java	…
WalkerManagerUnitTest.java	…