aaron 831d430025 Added a collection for storing GenomeLocs, that also has functions for removing by genomic region (that may span multiple GenomeLoc's in the collection), and adding regions, which are then merged with any overlapping regions. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@809 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-22 21:52:40 +00:00
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cmdLine	Disable support for short name values directly abutting their arguments.	2009-05-17 16:09:32 +00:00
fasta	Introduce new index-based fasta reader. Clean up MicroManager code, pushing necessary code back into TraversalEngine.	2009-04-24 19:40:21 +00:00
threading	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
BaseUtilsTest.java	Intermediate checking for evaluation -- now supports transition / transversion evaluation	2009-05-22 17:05:06 +00:00
GenomeLocSetTest.java	Added a collection for storing GenomeLocs, that also has functions for removing by genomic region (that may span multiple GenomeLoc's in the collection), and adding regions, which are then merged with any overlapping regions.	2009-05-22 21:52:40 +00:00
GenomeLocTest.java	Changed the assert code in the genome loc to throw exceptions, and deleted a function no one seems to be using.	2009-04-30 13:54:51 +00:00
MathUtilsTest.java	A more thorough test for multinomialProbability.	2009-05-01 06:27:05 +00:00
PathUtilsTest.java	Test class for PathUtils.	2009-05-21 19:31:22 +00:00
RefHangerTest.java	JUnit test for RefHanger	2009-05-01 20:11:14 +00:00