diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 1571de6f0..89a4b6012 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -658,7 +658,7 @@ public class GenomeAnalysisEngine {
         BAQ.DEFAULT_GOP = argCollection.BAQGOP;
 
         validateSuppliedReference();
-        referenceDataSource = openReferenceSequenceFile(argCollection.referenceFile);
+        setReferenceDataSource(argCollection.referenceFile);
 
         validateSuppliedReads();
         readsDataSource = createReadsDataSource(genomeLocParser, referenceDataSource.getReference());
@@ -852,15 +852,14 @@ public class GenomeAnalysisEngine {
     }
 
     /**
-     * Opens a reference sequence file paired with an index.
+     * Opens a reference sequence file paired with an index.  Only public for testing purposes
      *
      * @param refFile Handle to a reference sequence file.  Non-null.
      * @return A thread-safe file wrapper.
      */
-    private ReferenceDataSource openReferenceSequenceFile(File refFile) {
-        ReferenceDataSource ref = new ReferenceDataSource(refFile);
-        genomeLocParser = new GenomeLocParser(ref.getReference());
-        return ref;
+    public void setReferenceDataSource(File refFile) {
+        this.referenceDataSource = new ReferenceDataSource(refFile);
+        genomeLocParser = new GenomeLocParser(referenceDataSource.getReference());
     }
 
     /**
diff --git a/java/test/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java b/java/test/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java
index e8e3631d5..e36ce1d0c 100644
--- a/java/test/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java
@@ -37,6 +37,7 @@ import org.testng.annotations.BeforeMethod;
 
 import org.testng.annotations.Test;
 
+import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
@@ -55,6 +56,8 @@ public class TraverseDuplicatesUnitTest extends BaseTest {
     private SAMFileHeader header;
     private GenomeLocParser genomeLocParser;
     private GenomeAnalysisEngine engine;
+    private File refFile = new File(validationDataLocation + "Homo_sapiens_assembly17.fasta");
+
 
     @BeforeMethod
     public void doBefore() {
@@ -62,6 +65,7 @@ public class TraverseDuplicatesUnitTest extends BaseTest {
         genomeLocParser =new GenomeLocParser(header.getSequenceDictionary());
 
         engine = new GenomeAnalysisEngine();
+        engine.setReferenceDataSource(refFile);
         engine.setGenomeLocParser(genomeLocParser);
         
         obj.initialize(engine);
diff --git a/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java b/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java
index 72c9fd76c..fd0234be8 100755
--- a/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java
@@ -84,6 +84,7 @@ public class TraverseReadsUnitTest extends BaseTest {
         genomeLocParser = new GenomeLocParser(ref);
 
         engine = new GenomeAnalysisEngine();
+        engine.setReferenceDataSource(refFile);
         engine.setGenomeLocParser(genomeLocParser);
     }