From 860de05a7c81adad8a94518f103bc07a7cd055f8 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 28 Oct 2010 12:39:18 +0000
Subject: [PATCH] Bug fix for PL vs. GL in header.  PL now truly default output
 for UGv2

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4592 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/genotyper/GridSearchAFEstimation.java        | 2 +-
 .../playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
index db3a86045..581b3b6a0 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/GridSearchAFEstimation.java
@@ -127,7 +127,7 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
             HashMap<String, Object> attributes = new HashMap<String, Object>();
             attributes.put(VCFConstants.DEPTH_KEY, getFilteredDepth(contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup()));
 
-            GenotypeLikelihoods likelihoods = new GenotypeLikelihoods(GL.getLikelihoods());
+            GenotypeLikelihoods likelihoods = new GenotypeLikelihoods(GL.getLikelihoods(), UnifiedGenotyperV2.DEFAULT_GENOTYPE_LIKELIHOODS_KEY);
             attributes.put(likelihoods.getKey(), likelihoods.getAsString());
 
             calls.put(sample, new Genotype(sample, myAlleles, AFbasedGenotype.second, null, attributes, false));
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java
index 3d21a6b6e..833ed1423 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperV2.java
@@ -49,6 +49,8 @@ import java.io.PrintStream;
 @By(DataSource.REFERENCE)
 @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
 public class UnifiedGenotyperV2 extends LocusWalker<VariantCallContext, UnifiedGenotyperV2.UGStatistics> implements TreeReducible<UnifiedGenotyperV2.UGStatistics> {
+    public static final String DEFAULT_GENOTYPE_LIKELIHOODS_KEY = VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY;
+
 
     @ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
 
@@ -156,7 +158,7 @@ public class UnifiedGenotyperV2 extends LocusWalker<VariantCallContext, UnifiedG
         }
 
         // FORMAT and INFO fields
-        headerInfo.addAll(VCFUtils.getSupportedHeaderStrings(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY));
+        headerInfo.addAll(VCFUtils.getSupportedHeaderStrings(UnifiedGenotyperV2.DEFAULT_GENOTYPE_LIKELIHOODS_KEY));
 
         // FILTER fields
         if ( UAC.STANDARD_CONFIDENCE_FOR_EMITTING < UAC.STANDARD_CONFIDENCE_FOR_CALLING ||