ebanks 97618663ef Refactored and generalized the VCF header info code. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2346 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-13 21:02:45 +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	A bit of cleanup in preparation for Picard patch.	2009-12-08 16:09:04 +00:00
genotype	Refactored and generalized the VCF header info code.	2009-12-13 21:02:45 +00:00
sam	changes to fix and test the interval based traversals	2009-06-25 17:54:15 +00:00
threading	…
BaseUtilsTest.java	Added tests for mostFrequentBaseFraction() and reverseComplementString()	2009-06-09 00:53:45 +00:00
ExpandingArrayListTest.java	Updated recalibrator integration tests to use all three platforms as well as a bam with multi-platform reads intermingled. CountCovariates v2.0.1: Once again uses a read filter to filter out zero mapping quality reads. Added --sorted_output option to output the table recalibration file in sorted order	2009-11-23 19:51:36 +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	…
MergingIteratorTest.java	Updated recalibrator integration tests to use all three platforms as well as a bam with multi-platform reads intermingled. CountCovariates v2.0.1: Once again uses a read filter to filter out zero mapping quality reads. Added --sorted_output option to output the table recalibration file in sorted order	2009-11-23 19:51:36 +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