rpoplin 1d46de6d34 The old recalibrator is replaced with the refactored recalibrator. Added a version message to the logger output. These walkers start at version 2.0.0 ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2117 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-23 14:58:33 +00:00
..
bed	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
cmdLine	Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.	2009-09-29 22:23:19 +00:00
fasta	Fix issue Eric was seeing with java.lang.Error in unmap0.	2009-10-09 17:46:56 +00:00
genotype	Fixed the sample mix-up bug Kiran discovered, and added a unit test in the VCF reader class (Thanks for the good example files Kiran). Also renamed the toStringRepresentation function to toStringEncoding, and added a matching method in VCFGenotypeRecord.	2009-11-19 18:17:47 +00:00
sam	changes to fix and test the interval based traversals	2009-06-25 17:54:15 +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	The old recalibrator is replaced with the refactored recalibrator. Added a version message to the logger output. These walkers start at version 2.0.0	2009-11-23 14:58:33 +00:00
GenomeLocParserTest.java	fixed a bug I checked in that Eric found, for intervals with no start or stop coordinate. Now I owe Eric a cookie, and Milk Street is so far away. Damn.	2009-09-22 04:34:18 +00:00
GenomeLocSortedSetTest.java	a couple of light changes to GenomeLocSortedSet.	2009-09-23 20:38:53 +00:00
GenomeLocTest.java	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
GenotypeUtilsTest.java	Removing the AllelicVariant interface, which is replaced by the Variation interface.	2009-10-06 17:44:24 +00:00
ListUtilsTest.java	Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass.	2009-09-28 18:12:32 +00:00
MathUtilsTest.java	A more thorough test for multinomialProbability.	2009-05-01 06:27:05 +00:00
MergingIteratorTest.java	The old recalibrator is replaced with the refactored recalibrator. Added a version message to the logger output. These walkers start at version 2.0.0	2009-11-23 14:58:33 +00:00
PathUtilsTest.java	Test class for PathUtils.	2009-05-21 19:31:22 +00:00
UtilsTest.java	a convenience method to join a map into a single string, which I need for some VCF work. Added some documentation to the join method as well.	2009-11-17 16:50:01 +00:00