chartl dfa3c3b875 Added: ... SequenomToVCF - Takes a sequenom ped file and converts it to a VCF file with the proper metrics for QC. It's currently a rough draft, but is working as expected on a test ped file, which is included as an integration test. Modified: VCFGenotypeCall -- added a cloneCall() method that returns a clone of the call Hapmap2VCF -- removed a VCFGenotypeCall object that gets instantiated and modified but never used (caused me all kinds of confusion when I was basing SequenomToVCF off of it) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2554 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-11 17:17:21 +00:00
..
duplicates	forgot to update md5s	2009-12-29 20:31:29 +00:00
poolseq	Added - new tests (Hapmap was re-added)	2009-12-14 21:57:20 +00:00
varianteval	Fix to isReference() in VCFRecord. Change to VariantCounter to correctly counter only non-genotype variants, as well as update to VariantEvalWalker	2010-01-07 00:03:29 +00:00
variantstovcf	Added:	2010-01-11 17:17:21 +00:00
ClipReadsWalkersIntegrationTest.java	moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.	2009-12-29 07:40:48 +00:00
ConcordanceTruthTableTest.java	First revision of command-line argument support for GenotypeWriter. Also, fixed the damn build.	2009-12-20 19:19:23 +00:00
HapmapPoolAllelicInfoIntegrationTest.java	Hurrr -- this uses power as part of its output. Changes to the power calculation broke the md5s RIGHT AFTER I HAD FIXED THEM arghflrg.	2009-12-14 22:42:50 +00:00