Mark DePristo b4f482a421 NanoScheduled ActiveRegionTraversal and HaplotypeCaller ... -- Made CountReadsInActiveRegions Nano schedulable, confirming identical results for linear and nano results -- Made Haplotype NanoScheduled, requiring misc. changes in the map/reduce type so that the map() function returns a List<VariantContext> and reduce actually prints out the results to disk -- Tests for NanoScheduling -- CountReadsInActiveRegionsIntegrationTest now does NCT 1, 2, 4 with CountReadsInActiveRegions -- HaplotypeCallerParallelIntegrationTest does NCT 1,2,4 calling on 100kb of PCR free data -- Some misc. code cleanup of HaplotypeCaller -- Analysis scripts to assess performance of nano scheduled HC -- In order to make the haplotype caller thread safe we needed to use an AtomicInteger for the class-specific static ID counter in SeqVertex and MultiDebrujinVertex, avoiding a race condition where multiple new Vertex() could end up with the same id.		2013-05-13 11:09:02 -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	NanoScheduled ActiveRegionTraversal and HaplotypeCaller	2013-05-13 11:09:02 -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