ebanks 3ff6e3404e Alleles are now returned in a consistent order, so we can deal with tri-allelic sites ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4002 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-10 15:21:10 +00:00
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annotator	Alleles are now returned in a consistent order, so we can deal with tri-allelic sites	2010-08-10 15:21:10 +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	Adding command-line header to VA and VF	2010-08-08 05:21:15 +00:00
genotyper	Alleles are now returned in a consistent order, so we can deal with tri-allelic sites	2010-08-10 15:21:10 +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 the tiger team changes. LOD calculation modified. -qScale is back in case people need it.	2010-08-09 20:41:03 +00:00
variantutils	Alleles are now returned in a consistent order, so we can deal with tri-allelic sites	2010-08-10 15:21:10 +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