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Use filtered depth for Exact model (just like grid search) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4518 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-18 18:08:31 +00:00
parent d54d9880d7
commit 0fe504b748
1 changed files with 1 additions and 1 deletions
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java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -224,7 +224,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
HashMap<String, Object> attributes = new HashMap<String, Object>();
ArrayList<Allele> myAlleles = new ArrayList<Allele>();
attributes.put(VCFConstants.DEPTH_KEY, contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).size());
attributes.put(VCFConstants.DEPTH_KEY, getUnfilteredDepth(contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup()));
double qual;
double[] posteriors = GLs.get(sample).getPosteriors();