From f7bd4998fc42560d3c1561772c2e5d48b34dbe7f Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 19 Oct 2012 12:13:59 -0400
Subject: [PATCH] No need for dummy GLs

---
 .../gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
index 903e733ac..0e97c090c 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
@@ -136,7 +136,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
             likelihoodSums[i] = new LikelihoodSum(vc.getAlternateAllele(i));
 
         // based on the GLs, find the alternate alleles with the most probability; sum the GLs for the most likely genotype
-        final ArrayList<double[]> GLs = getGLs(vc.getGenotypes(), true);
+        final ArrayList<double[]> GLs = getGLs(vc.getGenotypes(), false);
         for ( final double[] likelihoods : GLs ) {
 
             final int PLindexOfBestGL = MathUtils.maxElementIndex(likelihoods);