aaron 36c98b9d6c added tools to test read based traversals using the artificial in-memory SAM file tools, and testing of the PrintReadsWalker ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@957 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-10 01:52:25 +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	added some more documentation to the GLF writer and it's supporting classes, and some other fixes	2009-06-02 14:53:58 +00:00
sam	added tools to test read based traversals using the artificial in-memory SAM file tools, and testing of the PrintReadsWalker	2009-06-10 01:52:25 +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	Added tests for mostFrequentBaseFraction() and reverseComplementString()	2009-06-09 00:53:45 +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