aaron 72ae81c6de VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include: ... - Tribble is included directly in the GATK repo; those who have access to commit to Tribble can now directly commit from the GATK directory from Intellij; command line users can commit from inside the tribble directory. - Hapmap ROD now in Tribble; all mentions have been switched over. - VariantContext does not know about GenomeLoc; use VariantContextUtils.getLocation(VariantContext vc) to get a genome loc. - VariantContext.getSNPSubstitutionType is now in VariantContextUtils. - This does not include the checked-in project files for Intellij; still running into issues with changes to the iml files being marked as changes by SVN I'll send out an email to GSAMembers with some more details. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3954 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-05 18:47:53 +00:00
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annotator	Fix for Kiran: since the Variant Annotator will re-annotate on top of existing annotations it makes sense to remove old headers if they conflict with the definitions being added by VA.	2010-08-05 06:44:39 +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	Moving G's MyHapScore to replace the old HapScore	2010-08-04 21:00:54 +00:00
indels	Removed hard-coded pointers to references	2010-08-04 17:59:37 +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	VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:	2010-08-05 18:47:53 +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