ebanks 1292c96e29 The cleaner now adds the OC (original cigar) and OS (original alignment start) tags as appropriate to reads that get realigned; this feature can be turned off. Also, improved integration tests (sorry, Kiran!). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3657 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-28 16:46:47 +00:00
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IndelRealignerIntegrationTest.java	The cleaner now adds the OC (original cigar) and OS (original alignment start) tags as appropriate to reads that get realigned; this feature can be turned off. Also, improved integration tests (sorry, Kiran!).	2010-06-28 16:46:47 +00:00
IndelRealignerPerformanceTest.java	Fixing up output for performance tests	2010-06-23 17:00:17 +00:00
RealignerTargetCreatorIntegrationTest.java	Make the target creator a rod walker (that allows reads) so that we can easily trigger the cleaner on only known indel sites. Adding an integration test to cover this case.	2010-06-28 13:28:37 +00:00
RealignerTargetCreatorPerformanceTest.java	Adding performance tests for the indel realigner; should take ~3 hours.	2010-04-11 04:45:22 +00:00