Mark DePristo b9a33d3c66 Split original and optimized ART into largely independent pieces ... -- Allows us to cleanly run old and new art, which now have different traversal behavior (on purpose). Split unit tests as well.		2013-01-11 15:17:18 -05:00
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datasources	LIBS can now (optionally) track the unique reads it uses from the underlying read iterator	2013-01-11 15:17:16 -05:00
downsampling	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
executive	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
iterators	Refactor LIBS into utils.locusiterator before refactoring	2013-01-11 15:17:16 -05:00
refdata	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
report	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
samples	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
traversals	Split original and optimized ART into largely independent pieces	2013-01-11 15:17:18 -05:00
walkers	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
CommandLineGATKUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
EngineFeaturesIntegrationTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
GenomeAnalysisEngineUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
MaxRuntimeIntegrationTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
WalkerManagerUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00