Eric Banks ebd5404124 Fixed the add functionality of GenomeLocSortedSet. ... * Fixed GenomeLocSortedSet.add() to ensure that overlapping intervals are detected and an exception is thrown. * Fixed GenomeLocSortedSet.addRegion() by merging it with the add() method; it now produces sorted inputs in all cases. * Cleaned up duplicated code throughout the engine to create a list of intervals over all contigs. * Added more unit tests for add functionality of GLSS. * Resolves GSA-775.		2013-02-28 23:31:00 -05:00
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datasources	Fixed the add functionality of GenomeLocSortedSet.	2013-02-28 23:31:00 -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	Added better error message for BAMs with bad read groups.	2013-02-27 16:02:56 -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	Updating TestNG to the latest version	2013-02-22 09:40:23 -05:00
traversals	Collapse the downsampling fork in the GATK engine	2013-01-28 01:50:30 -05:00
walkers	Fix runtime public -> protected dependencies in the test suite	2013-02-26 21:19:12 -05:00
CommandLineGATKUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
EngineFeaturesIntegrationTest.java	Fix runtime public -> protected dependencies in the test suite	2013-02-26 21:19:12 -05:00
GenomeAnalysisEngineUnitTest.java	ActivityProfile and ActiveRegions respects engine interval boundaries	2013-02-18 10:40:25 -05:00
MaxRuntimeIntegrationTest.java	Fix runtime public -> protected dependencies in the test suite	2013-02-26 21:19:12 -05:00
WalkerManagerUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00