gatk-3.8

Author	SHA1	Message	Date
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
Mauricio Carneiro	2a4ccfe6fd	Updated all JAVA file licenses accordingly GSATDG-5	2013-01-10 17:06:41 -05:00
Eric Banks	4543ece088	Fixing parsing of genomelocs that contain colons in the contig names (which is allowed by the spec) as reported on the forum. Added unit test for this case.	2012-11-27 11:00:33 -05:00
Khalid Shakir	c50274e02e	During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice. Moved flanking interval utilies to IntervalUtils with UnitTests.	2011-11-17 13:56:42 -05:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00