hanna 5e8c08ee63 Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-28 20:13:01 +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	Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...	2009-05-28 20:13:01 +00:00
glf	adding some objects we need for the GLF format.	2009-05-27 22:32:25 +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
GenomeLocSortedSetTest.java	Added back end code support for Sharding based on genomic location for reads. Changed the sharding	2009-05-26 20:57:46 +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