From 1e07e97b589eb73cebe5052fb656b3c54295b618 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 2 Mar 2012 13:30:17 -0500
Subject: [PATCH] Optimization: create allele list just once, not for each
 genotype

---
 .../sting/gatk/walkers/annotator/RankSumTest.java         | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index 3f555f780..00968943d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -43,15 +43,15 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
         final ArrayList<Double> altQuals = new ArrayList<Double>();
 
         if ( vc.isSNP() ) {
+            final List<Byte> altAlleles = new ArrayList<Byte>();
+            for ( final Allele a : vc.getAlternateAlleles() )
+                altAlleles.add(a.getBases()[0]);
+
             for ( final Genotype genotype : genotypes.iterateInSampleNameOrder() ) {
                 final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
                 if ( context == null )
                     continue;
 
-                final List<Byte> altAlleles = new ArrayList<Byte>();
-                for ( final Allele a : vc.getAlternateAlleles() )
-                    altAlleles.add(a.getBases()[0]);
-                
                 fillQualsFromPileup(ref.getBase(), altAlleles, context.getBasePileup(), refQuals, altQuals);
             }
         } else if ( vc.isIndel() || vc.isMixed() ) {