From 5e29d0c2191ba7bbb2bbca488dd467278d296a9a Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 17 Mar 2010 17:35:23 +0000
Subject: [PATCH] Be smarter about dealing with infinite quals for ref calls

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3024 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../genotyper/JointEstimateGenotypeCalculationModel.java     | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
index 63272f3a4..6199589d1 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
@@ -337,8 +337,11 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
             phredScaledConfidence = QualityUtils.phredScaleErrorRate(PofFs[indexOfMax]);
             if ( Double.isInfinite(phredScaledConfidence) ) {
                 double sum = 0.0;
-                for (int i = 1; i < frequencyEstimationPoints; i++)
+                for (int i = 1; i < frequencyEstimationPoints; i++) {
+                    if ( log10PofDgivenAFi[indexOfMax][i] == VALUE_NOT_CALCULATED )
+                        break;
                     sum += log10PofDgivenAFi[indexOfMax][i];
+                }
                 phredScaledConfidence = -10.0 * sum;
             }
         }