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7 Commits (3380b6ebe808bb7c5630dcdabafb446fb8d5d094)

Author SHA1 Message Date
ebanks 6c739e30e0 1. Removing an old version of the Genotype interface which is no longer being used. Needed to do this now so that the naming conflicts would cease. 
2. Adding a preliminary version of the new Genotype/Allele interface (putting it into refdata/ as the VariantContext really only applies to rods) with updates to VariantContext.  This is by no means complete - further updates coming tomorrow.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2533 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 05:51:10 +00:00
ebanks fdd14e1a01 Proposed interface for VariantContext. It's currently an interface so it doesn't break the build... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2521 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 16:31:39 +00:00
ebanks 797bb83209 New VariantFiltration. 
Wiki docs are updated.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2105 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-20 19:50:26 +00:00
depristo d316cbad4c VariantFilteration now accepts a VCF rod in addition to an input geli. It will then annotate this VCF file with filtering information in the INFO field too. --OnlyAnnotate will not write in filtering output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2008 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 13:24:58 +00:00
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