ebanks 4e85416af1 [Foiled yet again when trying to do this in git] Slight modifications in the argument structure for the IndelRealigner. Instead of boolean flags -knownsOnly and -doNotUseSW, we now have an enum --consensusDeterminationModel which lets you specify knowns only, also use indels in reads, or also use SW. Please note that the default behavior of IR has not changed at all (and won't for a few more days) - that'll be done in GIT (fingers crossed). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6008 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-16 17:35:37 +00:00
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IndelRealignerIntegrationTest.java	[Foiled yet again when trying to do this in git] Slight modifications in the argument structure for the IndelRealigner. Instead of boolean flags -knownsOnly and -doNotUseSW, we now have an enum --consensusDeterminationModel which lets you specify knowns only, also use indels in reads, or also use SW. Please note that the default behavior of IR has not changed at all (and won't for a few more days) - that'll be done in GIT (fingers crossed).	2011-06-16 17:35:37 +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