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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varianteval	Updated integration tests for VariantEval. Hooray for IT!	2009-10-16 20:00:29 +00:00
variantstovcf	changes to VCF output, and updated MD5's in the integration tests	2009-10-14 18:42:48 +00:00
BaseTransitionTableCalculatorJavaIntegrationTest.java	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
ClipReadsWalkersIntegrationTest.java	Softclipping support in clip reads walker. Minor improvement to WalkerTest -- now can specify file extensions for tmp files. Matt -- I couldn't easily create non-presorted SAM file. The softclipper has an impact on this.	2009-10-19 21:54:53 +00:00