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gatk-3.8/java/test/org/broadinstitute/sting
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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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alignment Quick fix for Danny Lieber: flesh out the additional functionality required 2011-01-31 05:28:37 +00:00
commandline Fixed long-standing bug reported by Mauricio where @Arguments assigned to 2011-01-12 22:18:24 +00:00
datasources/pipeline Removed deprecated getDbsnpFile. 2011-02-08 21:12:15 +00:00
gatk 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
jna Added pipeline for calling FCP in batches called MultiFullCallingPipeline. 2011-02-15 18:26:14 +00:00
oneoffprojects/walkers Structural refactoring in advance of dichotomization statistics; generalization of statistical test infrastructure. 2011-04-05 18:52:32 +00:00
playground/gatk/walkers 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
utils Enabled the parameterize option for debugging PipelineTest MD5s. 2011-03-26 00:41:47 +00:00
BaseTest.java Added pipeline for calling FCP in batches called MultiFullCallingPipeline. 2011-02-15 18:26:14 +00:00
StingTextReporter.java Cleanup testng listener configuration. 2010-11-15 23:43:14 +00:00
WalkerTest.java When subsetting by sample, need to take extra care that hom-ref sites don't accidentally get treated as variant sites in CompOverlap. Renamed convenience method for creating command-lines in integration tests. 2011-02-18 06:26:38 +00:00