diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProvider.java b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProvider.java
index 2c1b4d755..d913c04c3 100755
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProvider.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProvider.java
@@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import net.sf.samtools.SAMRecord;
 /**
  * User: hanna
  * Date: May 8, 2009
@@ -107,6 +108,15 @@ public class ShardDataProvider {
         return referenceProvider.getReferenceBase(genomeLoc);        
     }
 
+    /**
+     * Gets the reference base associated with this particular point on the genome.
+     * @param read the read to fetch the reference sequence for
+     * @return a char string of bases representing the reference sequence corresponding to passed in read
+     */
+    public char[] getReferenceForRead( SAMRecord read ) {
+        return referenceProvider.getReferenceBases(read);
+    }
+
     /**
      * Create a data provider for the shard given the reads and reference.
      * @param shard The chunk of data over which traversals happen.
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
index 83d1b95a4..13cabb476 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
@@ -95,21 +95,23 @@ public class TraverseReads extends TraversalEngine {
             // our locus context
             LocusContext locus = null;
 
+            // an array of characters that represent the reference
+            char[] refSeq = null;
+
             if (read.getReferenceIndex() >= 0) {
                 // get the genome loc from the read
                 GenomeLoc site = new GenomeLoc(read);
 
                 // Jump forward in the reference to this locus location
                 locus = new LocusContext(site, Arrays.asList(read), Arrays.asList(0));
+
+                // get the array of characters for the reference sequence, since we're a mapped read
+                refSeq = dataProvider.getReferenceForRead( read );
             }
 
             // update the number of reads we've seen
             TraversalStatistics.nRecords++;
 
-
-            // we still have to fix the locus context provider to take care of this problem with > 1 length contexts
-            // LocusContext locus = locusProvider.getLocusContext(site);
-
             final boolean keepMeP = readWalker.filter(locus, read);
             if (keepMeP) {
                 M x = readWalker.map(locus, read);
@@ -118,7 +120,6 @@ public class TraverseReads extends TraversalEngine {
 
             if (locus != null) { printProgress("loci", locus.getLocation()); }
         }
-        //System.err.println(TraversalStatistics.nRecords);
         return sum;
     }