- GATKVCFWriter deleted, to be replaced if absolutely necessary when VCF writing goes into Tribble.
- VCFWriter is now an interface, for easier redirection.
- VCFWriterImpl fleshes out the VCFWriter interface.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4026 348d0f76-0448-11de-a6fe-93d51630548a
- 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
2) Keep track of whether vcf records are unfiltered vs. pass filters in the variant context so we can regenerate the records on output.
3) No more "ID" hard-coded all over the code to set the VariantContext ID. Use a static variable instead.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3840 348d0f76-0448-11de-a6fe-93d51630548a
Provides a cleaner interface with extended events inheriting all of the basic RBP
functionality. Implementation is still slightly messy, but should allow users to
provide separate implementations of methods for sample split pileups and unsplit
pileups for efficiency's sake.
Methods not covered by unit/integration tests have not been sufficiently tested yet.
Unit tests will follow this week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3597 348d0f76-0448-11de-a6fe-93d51630548a
hanna
ebanks
aaron
delangel
chartl