chartl af761fb9bd Base transition table now forces epsilon/3 (three-state) model for the unified genotyper. Verified to be identical with changing the default model to being epsilon/3. This of course changes the observed counts, so the integration test has been updated. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1897 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-21 21:18:26 +00:00
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gatk	ensure that in the indel case we don't allow identification as both an insertion and deletion at the same location in the VCF ROD	2009-10-19 18:21:00 +00:00
playground/gatk/walkers	Base transition table now forces epsilon/3 (three-state) model for the unified genotyper. Verified to be identical with changing the default model to being epsilon/3. This of course changes the observed counts, so the integration test has been updated.	2009-10-21 21:18:26 +00:00
utils	Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.	2009-10-20 12:23:36 +00:00
BaseTest.java	Added some code to change the instrumentation for tests.	2009-05-20 05:15:27 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00
WalkerTest.java	Enabling correct high-performance ROD walker and moved VariantEval over to it. Performance improvements in variantEval in general. See wiki for full description	2009-10-20 23:31:13 +00:00