ebanks 5f3c80d9aa 1. To make indel calls, we need to get rid of the SNP-centricity of our code. First step is to have the reference be a String, not a char in the Genotype. Note that this is just a temporary patch until the genotype code is ported over to use VariantContext. ... 2. Significant refactoring of Plink code to work in the rods and use VariantContext. More coming. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2913 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-02 20:26:40 +00:00
..
bed	Looks bigger than it is:	2010-01-15 00:14:35 +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	moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.	2009-12-29 07:40:48 +00:00
genotype	1. To make indel calls, we need to get rid of the SNP-centricity of our code. First step is to have the reference be a String, not a char in the Genotype. Note that this is just a temporary patch until the genotype code is ported over to use VariantContext.	2010-03-02 20:26:40 +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	V5 improvements to VariantContext. Now fully supports genotypes. Filtering enabled. Significant tests throughout system. Support for rebuilding variant contexts from subsets of genotypes. Some code cleanup around repository	2010-01-28 18:37:17 +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	added methods to validate an interval before you try to make a GenomeLoc: boolean validGenomeLoc().	2010-02-16 20:35:35 +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
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
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