From 0fe504b7488bbaa7ec945c92c9fad89875bc5d0a Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 18 Oct 2010 18:08:31 +0000
Subject: [PATCH] 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
---
 .../gatk/walkers/genotyper/ExactAFCalculationModel.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
index 78f99ddf8..88aeb7f6d 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
@@ -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();