Mark DePristo 45603f58cd Refactoring and unit testing GenomeLocParser ... -- Moved previously inner class to MRUCachingSAMSequenceDictionary, and unit test to 100% coverage -- Fully document all functions in GenomeLocParser -- Unit tests for things like parsePosition (shocking it wasn't tested!) -- Removed function to specifically create GenomeLocs for VariantContexts. The fact that you must incorporate END attributes in the context means that createGenomeLoc(Feature) works correctly -- Depreciated (and moved functionality) of setStart, setStop, and incPos to GenomeLoc -- Unit test coverage at like 80%, moving to 100% with next commit		2013-01-30 09:47:47 -05:00
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net/sf	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
org/broadinstitute	Refactoring and unit testing GenomeLocParser	2013-01-30 09:47:47 -05:00