depristo bbd7bec5db Continuing cleanup of SSG. GenotypeLikelihoods now have extensive testing routines. DiploidGenotype supports het, homref, etc calculations. SSG has been cleaned up to remove old garbage functionality. Also now supports output to standard output by simply omitting varout ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1387 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-05 22:25:30 +00:00
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datasources	Windowed access to the reference.	2009-08-05 16:29:15 +00:00
executive	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +00:00
iterators	an iterator to fix the problem where read-based interval traversals are getting duplicate reads because reads span the two intervals.	2009-07-23 23:59:48 +00:00
refdata	Adding the intial changes for the new Genotyping interface. The bullet points are:	2009-07-29 19:43:59 +00:00
traversals	Refactoring of the traversal engine base class, I removed a lot of old code.	2009-07-09 21:57:00 +00:00
walkers	Continuing cleanup of SSG. GenotypeLikelihoods now have extensive testing routines. DiploidGenotype supports het, homref, etc calculations. SSG has been cleaned up to remove old garbage functionality. Also now supports output to standard output by simply omitting varout	2009-08-05 22:25:30 +00:00
GATKArgumentCollectionTest.java	Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing.	2009-07-08 20:26:16 +00:00
OutputTrackerTest.java	Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*	2009-07-29 16:11:45 +00:00