depristo 8ac40e8e2d Updated version of the recalibration tool ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-19 17:45:47 +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
genotype/glf	a rename for consistancy of Sam to SAM, creating a genotype utils dir, and moving the GLF code into it.	2009-06-11 17:46:06 +00:00
sam	added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance.	2009-06-16 22:15:56 +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
ExpandingArrayListTest.java	Updated version of the recalibration tool	2009-06-19 17:45:47 +00:00
GenomeLocSortedSetTest.java	a rename for consistancy of Sam to SAM, creating a genotype utils dir, and moving the GLF code into it.	2009-06-11 17:46:06 +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