rpoplin 3f3f35dea0 UnifiedGenotyper now BAQs via ADD_TAG to facilitate using BAQed quals for GL calculations but unBAQed quals for annotation calculations. UnifiedGenotyper now produces SNP and indel calls simultaneously. 40 base mismatch intrinsic filter removed from UG to greatly simplify the code. RankSumTests are now standard annotations but the integration tests are commented out pending changes that will allow random annotations to work. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5585 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-06 19:06:24 +00:00
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HLAcaller	Committing the fragment-based calling code. Results look great in all datasets (will show this at 1000G this week with Ryan). Note that this is an intermediate commit. The code needs to be cleaned up and the fragmentation code needs to be moved up into LocusIteratorByState. This should all happen later this week, but I don't want Ryan to have to keep running from my own personal Sting directory. The current crappy implementation adds ~10% to the runtime, but that should all go away in the next iteration.	2011-01-23 05:04:17 +00:00
duplicates	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
validation	consolidating the checking of the RMD sequence dictionary against the reference into a single function, and adding an integration test to test that empty VCFs pass (both the indexing and the seq dictionary validation).	2010-11-30 00:01:56 +00:00
variantrecalibration	UnifiedGenotyper now BAQs via ADD_TAG to facilitate using BAQed quals for GL calculations but unBAQed quals for annotation calculations. UnifiedGenotyper now produces SNP and indel calls simultaneously. 40 base mismatch intrinsic filter removed from UG to greatly simplify the code. RankSumTests are now standard annotations but the integration tests are commented out pending changes that will allow random annotations to work.	2011-04-06 19:06:24 +00:00