ebanks ac4699a650 Re-enabling this test ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3962 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-06 20:20:37 +00:00
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annotator	1) AlleleBalance is no longer a standard annotation, but the Allelic Depth (AD) is for each sample.	2010-08-06 12:05:14 +00:00
coverage	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
fasta	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
filters	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
genotyper	1) AlleleBalance is no longer a standard annotation, but the Allelic Depth (AD) is for each sample.	2010-08-06 12:05:14 +00:00
indels	Re-enabling this test	2010-08-06 20:20:37 +00:00
qc	Fixed epic generic paths fail.	2010-05-13 15:59:57 +00:00
recalibration	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
sequenom	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
varianteval	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
variantrecalibration	Checking in everyone's changes to the variant recalibrator. We now calculate the variant quality score as a LOD score between the true and false hypothesis. Allele Count prior is changed to be (1 - 0.5^ac). Known prior breaks out HapMap sites	2010-08-05 14:12:19 +00:00
variantutils	-minimalVCF for CombineVariants. Work around for broken locking code.	2010-08-06 16:10:59 +00:00
PileupWalkerIntegrationTest.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
PrintReadsWalkerUnitTest.java	Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK	2010-05-19 23:27:55 +00:00
VariantsToVCFIntegrationTest.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00