From 6c0adc91455629395348cad8cbd71c63046fe9b9 Mon Sep 17 00:00:00 2001
From: kcibul <kcibul@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 20 Aug 2009 16:01:58 +0000
Subject: [PATCH] resuse fasta file reader

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1446 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/HybSelPerformanceWalker.java    | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
index d0d28601c..05bd37ec5 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
@@ -170,9 +170,13 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
         return new Interval(target.getContig(), (int) target.getStart(), (int) target.getStop());
     }
 
+    IndexedFastaSequenceFile seqFile = null;
+
     private double calculateGC(GenomeLoc target) {
         try {
-            IndexedFastaSequenceFile seqFile = new IndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
+            if (seqFile == null) {
+                seqFile = new IndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
+            }
             ReferenceSequence refSeq = seqFile.getSubsequenceAt(target.getContig(),target.getStart(), target.getStop());