ebanks 15c7bd82a5 Fix for IndelRealigner memory problem. Now the Constrained mate fixing writer is told whether a read has been modified and, if it wasn't, can dump it when the cache needs to get flushed at places with tons of coverage. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5777 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-06 19:34:41 +00:00
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IndelRealignerIntegrationTest.java	Fix for IndelRealigner memory problem. Now the Constrained mate fixing writer is told whether a read has been modified and, if it wasn't, can dump it when the cache needs to get flushed at places with tons of coverage.	2011-05-06 19:34:41 +00:00
IndelRealignerPerformanceTest.java	New attempt at the constrained movement version of the indel realigner (I've kept around the old writer for now). The new contract is that the realigner must ask permission before trying to clean an area; permission will be denied by the CM-Manager if it was required to flush its cache of reads because of too much depth within a distance of maxInsertSizeForMovingReadPairs. Added integration tests to cover different max cache sizes, including an expected exception when too small a value is chosen. The actual logic changes were fairly minor - much of this commit is really just some cleanup. I'd like to throw 1000G Phase I at it, but will respectfully wait for Ryan to hit his deadline before doing so.	2011-03-10 02:48:29 +00:00
RealignerTargetCreatorIntegrationTest.java	Updating integration test to be in sync with previous commit	2011-02-24 20:21:58 +00:00
RealignerTargetCreatorPerformanceTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00