From a9472c198061f5127225e8e632a9a97dd5c40985 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Mon, 20 Aug 2012 16:11:45 -0400
Subject: [PATCH] Another round of FindBugs fixes. Inefficient use of keySet
 iterator instead of entrySet iterator.

---
 .../walkers/haplotypecaller/LikelihoodCalculationEngine.java  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index b5ce4b4bc..a69e39401 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -77,10 +77,10 @@ public class LikelihoodCalculationEngine {
         PairHMM.initializeArrays(matchMetricArray, XMetricArray, YMetricArray, X_METRIC_LENGTH);
 
         // for each sample's reads
-        for( final String sample : perSampleReadList.keySet() ) {
+        for( final Map.Entry<String, ArrayList<GATKSAMRecord>> sampleEntry : perSampleReadList.entrySet() ) {
             //if( DEBUG ) { System.out.println("Evaluating sample " + sample + " with " + perSampleReadList.get( sample ).size() + " passing reads"); }
             // evaluate the likelihood of the reads given those haplotypes
-            computeReadLikelihoods( haplotypes, perSampleReadList.get(sample), sample, matchMetricArray, XMetricArray, YMetricArray );
+            computeReadLikelihoods( haplotypes, sampleEntry.getValue(), sampleEntry.getKey(), matchMetricArray, XMetricArray, YMetricArray );
         }
     }