gatk-3.8

Author	SHA1	Message	Date
depristo	6231637615	fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2213 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-02 15:41:35 +00:00
chartl	21a9a717e4	Some minor changes and test: - DepthOfCoverage is now by reference (so locus-by-locus output correctly reports zero-coverage bases) - VariantsToVCF now lets you bind variants with any string except intervals and dbsnp (not just NA######) - A PileupWalker integration test on a particularly nasty FHS site - Two second-base annotation related integration tests on that same site + outputs were all hand-validated in matlab; within a certain tolerance for the annotations git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2197 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-01 15:15:54 +00:00

Author

SHA1

Message

Date

depristo

fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2213 348d0f76-0448-11de-a6fe-93d51630548a

2009-12-02 15:41:35 +00:00

chartl

21a9a717e4

Some minor changes and test:

- DepthOfCoverage is now by reference (so locus-by-locus output correctly reports zero-coverage bases)
  - VariantsToVCF now lets you bind variants with any string except intervals and dbsnp (not just NA######)
  - A PileupWalker integration test on a particularly nasty FHS site
  - Two second-base annotation related integration tests on that same site
       + outputs were all hand-validated in matlab; within a certain tolerance for the annotations




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2197 348d0f76-0448-11de-a6fe-93d51630548a

2009-12-01 15:15:54 +00:00

2 Commits (6231637615657e5fe87e8b91cd278db519d966f1)