hanna 8573b0bc6f Refactoring intervals, separating the process of parsing interval lists, ... sorting and merging interval lists, and creating RODs from intervals. This gives Doug the ability to keep using our interval list parsing code when sorting intervals on our behalf. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3159 348d0f76-0448-11de-a6fe-93d51630548a		2010-04-13 15:50:38 +00:00
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alignment	Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath.	2010-04-01 17:17:16 +00:00
gatk	Generalizing the SequenomValidationConverter to be able to take in any arbitrary rod type (provided it can be converted to VariantContext).	2010-04-12 20:42:18 +00:00
oneoffprojects/walkers/varianteval2	Variant Quality Score modules in VariantEval2 no longer create huge lists which hold all of the quality scores encountered and instead cast the quality score to an integer and use hash tables. Bug fix for files in which all the quality scores are set to -1.	2010-04-09 18:36:06 +00:00
playground	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.	2010-04-08 06:14:15 +00:00
utils	Refactoring intervals, separating the process of parsing interval lists,	2010-04-13 15:50:38 +00:00
BaseTest.java	Adding performance tests for the recalibrator (Whole Genome and Whole Exome tests).	2010-04-09 18:30:59 +00:00
WalkerTest.java	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.	2010-04-08 06:14:15 +00:00