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3 Commits (f9819d5f1368d04008ffa364ca1592a7a77ff670)

Author SHA1 Message Date
aaron 0cc634ed5d -Renamed rodVariants to RodGeliText 
-Remove KGenomesSNPROD
-Remove rodFLT
-Renamed rodGFF to RodGenotypeChipAsGFF
-Fixed a problem in SSGenotypeCall
-Added basic SSGenotype Test class
-Make VCFHeader constructors public

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1536 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 18:40:43 +00:00
ebanks 1a299dd459 Require each filter or feature to declare whether or not they want mapping quality zero reads in the alignment context 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1486 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-31 03:31:37 +00:00
ebanks 215e908a11 Reworking of the VariantFiltration system to allow for a windowed view of variants and inclusion of more data to the various filters. 
This now allows us to incorporate both the clustered SNP filter and a SNP-near-indels filter, which otherwise wasn't possible.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1484 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-31 02:16:39 +00:00