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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net/sf/picard/reference	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +00:00
org/broadinstitute/sting	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