hanna 71e3825fa1 First pass of a walker for Eric that searches through an input BAM file for unclean reads, injecting the cleaned reads in their place and outputting the composite result. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@989 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-11 20:18:13 +00:00
..
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	First pass of a walker for Eric that searches through an input BAM file for unclean reads, injecting the cleaned reads in their place and outputting the composite result.	2009-06-11 20:18:13 +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	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