From 7ff8d23c649864c14fa0f89645fab4451d0203dc Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 25 Feb 2011 21:11:50 +0000
Subject: [PATCH] Don't do genotype concordance on comp tracks without
 genotypes, even if they have an AC

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5321 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/varianteval/evaluators/GenotypeConcordance.java   | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
index 0fdef754f..66204e24b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
@@ -249,7 +249,7 @@ public class GenotypeConcordance extends VariantEvaluator {
         String interesting = null;
 
         // sanity check that we at least have either eval or validation data
-        if (eval == null && !isValidVC(validation)) {
+        if ( (validation != null && !validation.hasGenotypes()) || eval == null && !isValidVC(validation)) {
             return interesting;
         }
 
@@ -300,7 +300,6 @@ public class GenotypeConcordance extends VariantEvaluator {
     }
 
     private String determineStats(final VariantContext eval, final VariantContext validation) {
-
         String interesting = null;
 
         final boolean validationIsValidVC = isValidVC(validation);
@@ -380,7 +379,6 @@ public class GenotypeConcordance extends VariantEvaluator {
             } else { // multi sample calls
                 qualityScoreHistograms.incrValue( eval.getPhredScaledQual(), validation.isPolymorphic() );
             }
-
         }
 
         return interesting;