gatk-3.8

Author	SHA1	Message	Date
hanna	80b3eb85fa	Fixed curiously epic failure in read-backed pileup: size() mismatched the numReads-numDeletions at that locus in the case where includeReadsWithDeletionsAtLoci == false, causing failures including bad output from pileup walker. Also fixed up ValidatingPileup to run with the new ReadBackedPileup instead of just compiling successfully. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2409 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-18 22:52:44 +00:00
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

hanna

Fixed curiously epic failure in read-backed pileup: size() mismatched the numReads-numDeletions at that locus in the case where includeReadsWithDeletionsAtLoci == false, causing failures including bad output from pileup walker. Also fixed up ValidatingPileup to run with the new ReadBackedPileup instead of just compiling successfully.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2409 348d0f76-0448-11de-a6fe-93d51630548a

2009-12-18 22:52:44 +00:00

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

3 Commits (2bd0b1bbf7279d0dd4e6ca03d8cff6dea13bf9c3)