diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index c142109fa..803bf514c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -180,12 +180,12 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
             final Haplotype haplotype1 = consensusHaplotypeQueue.poll();
 
             List<Haplotype>hlist = new ArrayList<Haplotype>();
-            hlist.add(new Haplotype(haplotype1.getBasesAsBytes(), 60));
+            hlist.add(new Haplotype(haplotype1.getBases(), 60));
 
             for (int k=1; k < haplotypesToCompute; k++) {
                 Haplotype haplotype2 = consensusHaplotypeQueue.poll();
                 if(haplotype2 == null ) { haplotype2 = haplotype1; } // Sometimes only the reference haplotype can be found
-                hlist.add(new Haplotype(haplotype2.getBasesAsBytes(), 20));
+                hlist.add(new Haplotype(haplotype2.getBases(), 20));
             }
             return hlist;
         } else
@@ -229,8 +229,8 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
     }
 
     private Haplotype getConsensusHaplotype(final Haplotype haplotypeA, final Haplotype haplotypeB) {
-        final byte[] a = haplotypeA.getBasesAsBytes();
-        final byte[] b = haplotypeB.getBasesAsBytes();
+        final byte[] a = haplotypeA.getBases();
+        final byte[] b = haplotypeB.getBases();
 
         if (a.length != b.length) {
             throw new ReviewedStingException("Haplotypes a and b must be of same length");
@@ -313,7 +313,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
         // actually be a miscall in a matching direction, which would happen at a e / 3 rate.  If b != c, then
         // the chance that it is actually a mismatch is 1 - e, since any of the other 3 options would be a mismatch.
         // so the probability-weighted mismatch rate is sum_i ( matched ? e_i / 3 : 1 - e_i ) for i = 1 ... n
-        final byte[] haplotypeBases = haplotype.getBasesAsBytes();
+        final byte[] haplotypeBases = haplotype.getBases();
         final SAMRecord read = p.getRead();
         byte[] readBases = read.getReadBases();
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
index 3b3f54b05..200a250f2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
@@ -205,7 +205,7 @@ public class HaplotypeIndelErrorModel {
 
                 byte haplotypeBase;
                 if (haplotypeIndex < RIGHT_ALIGN_INDEX)
-                    haplotypeBase = haplotype.getBasesAsBytes()[haplotypeIndex];
+                    haplotypeBase = haplotype.getBases()[haplotypeIndex];
                 else
                     haplotypeBase = (byte)0; // dummy
 
@@ -217,7 +217,7 @@ public class HaplotypeIndelErrorModel {
                 if (readQual > 3)
                     pRead += pBaseRead;
                 haplotypeIndex++;
-                if (haplotypeIndex >= haplotype.getBasesAsBytes().length)
+                if (haplotypeIndex >= haplotype.getBases().length)
                     haplotypeIndex = RIGHT_ALIGN_INDEX;
                 //System.out.format("H:%c R:%c RQ:%d HI:%d %4.5f %4.5f\n", haplotypeBase, readBase, (int)readQual, haplotypeIndex, pBaseRead, pRead);
              }
@@ -227,8 +227,8 @@ public class HaplotypeIndelErrorModel {
                 System.out.println(read.getReadName());
                 System.out.print("Haplotype:");
 
-                for (int k=0; k <haplotype.getBasesAsBytes().length; k++) {
-                    System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
+                for (int k=0; k <haplotype.getBases().length; k++) {
+                    System.out.format("%c ", haplotype.getBases()[k]);
                 }
                 System.out.println();
 
@@ -246,8 +246,8 @@ public class HaplotypeIndelErrorModel {
 
                 System.out.println("Haplotype:");
 
-                for (int k=initialIndexInHaplotype; k <haplotype.getBasesAsBytes().length; k++) {
-                    System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
+                for (int k=initialIndexInHaplotype; k <haplotype.getBases().length; k++) {
+                    System.out.format("%c ", haplotype.getBases()[k]);
                 }
                 System.out.println();
 
@@ -275,7 +275,7 @@ public class HaplotypeIndelErrorModel {
 
                 byte haplotypeBase;
                 if (indX > LEFT_ALIGN_INDEX && indX < RIGHT_ALIGN_INDEX)
-                    haplotypeBase = haplotype.getBasesAsBytes()[indX-1];
+                    haplotypeBase = haplotype.getBases()[indX-1];
                 else
                     haplotypeBase = readBase;
 
@@ -296,8 +296,8 @@ public class HaplotypeIndelErrorModel {
             System.out.println(read.getReadName());
             System.out.print("Haplotype:");
 
-            for (int k=0; k <haplotype.getBasesAsBytes().length; k++) {
-                System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
+            for (int k=0; k <haplotype.getBases().length; k++) {
+                System.out.format("%c ", haplotype.getBases()[k]);
             }
             System.out.println();
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 11ff99ce3..b28980d9c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -381,7 +381,7 @@ public class PairHMMIndelErrorModel {
         // todo -- refactor into separate function
         for (Allele a: haplotypeMap.keySet()) {
             Haplotype haplotype = haplotypeMap.get(a);
-            byte[] haplotypeBases = haplotype.getBasesAsBytes();
+            byte[] haplotypeBases = haplotype.getBases();
             double[] contextLogGapOpenProbabilities = new double[haplotypeBases.length];
             double[] contextLogGapContinuationProbabilities = new double[haplotypeBases.length];
 
@@ -555,7 +555,7 @@ public class PairHMMIndelErrorModel {
                         long indStart = start - haplotype.getStartPosition();
                         long indStop =  stop - haplotype.getStartPosition();
 
-                        byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBasesAsBytes(),
+                        byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(),
                                 (int)indStart, (int)indStop);
 
                         double readLikelihood;
diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
index ce2ca2c28..df682f215 100755
--- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
@@ -33,8 +33,8 @@ import java.util.LinkedHashMap;
 import java.util.List;
 
 public class Haplotype {
-    protected byte[] bases = null;
-    protected double[] quals = null;
+    protected final byte[] bases;
+    protected final double[] quals;
     private GenomeLoc genomeLocation = null;
     private boolean isReference = false;
  
@@ -69,6 +69,11 @@ public class Haplotype {
         this.isReference = isRef;
     }
 
+    @Override
+    public boolean equals( Object h ) {
+        return h instanceof Haplotype && Arrays.equals(bases, ((Haplotype) h).bases);
+    }
+
     public double getQualitySum() {
         double s = 0;
         for (int k=0; k < bases.length; k++) {
@@ -88,7 +93,7 @@ public class Haplotype {
     public double[] getQuals() {
         return quals;
     }
-    public byte[] getBasesAsBytes() {
+    public byte[] getBases() {
         return bases;
     }
 
@@ -100,7 +105,6 @@ public class Haplotype {
         return genomeLocation.getStop();
     }
 
-
     public boolean isReference() {
         return isReference;
     }