diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index bfa1c4db5..d27fec8fb 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -44,7 +44,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
 public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
     private final static boolean DEBUG = false;
     private final static int MIN_CONTEXT_WING_SIZE = 10;
-    private final static String REGEXP_WILDCARD = ".";
+    private final static char REGEXP_WILDCARD = '.';
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( !vc.isBiallelic() || !vc.isSNP() || stratifiedContexts.size() == 0 ) // size 0 means that call was made by someone else and we have no data here
@@ -82,7 +82,6 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
         }
     }
 
-
     private List<Haplotype> computeHaplotypes(ReadBackedPileup pileup, int contextSize) {
         // Compute all possible haplotypes consistent with current pileup
         ArrayList<Haplotype> haplotypeList = new ArrayList<Haplotype>();
@@ -168,7 +167,7 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
         byte[] haplotypeBases = new byte[contextSize];
 
         for(int i=0; i < contextSize; i++) {
-            haplotypeBases[i] = REGEXP_WILDCARD.getBytes()[0];
+            haplotypeBases[i] = (byte)REGEXP_WILDCARD;
         }
 
         double[] baseQualities = new double[contextSize];
@@ -185,30 +184,26 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
             baseQualities[i] = (double)read.getBaseQualities()[baseOffset];
         }
 
-
         return new Haplotype(haplotypeBases, baseQualities);
-
     }
 
-
-
     private Haplotype getConsensusHaplotype(Haplotype haplotypeA, Haplotype haplotypeB) {
-        String a = haplotypeA.toString();
-        String b = haplotypeB.toString();
+        byte[] a = haplotypeA.getBasesAsBytes();
+        byte[] b = haplotypeB.getBasesAsBytes();
 
-        if (a.length() != b.length())
+        if (a.length != b.length)
             throw new ReviewedStingException("Haplotypes a and b must be of same length");
 
-        char chA, chB;
-        char wc = REGEXP_WILDCARD.charAt(0);
+        byte chA, chB;
+        byte wc = (byte)REGEXP_WILDCARD;
 
+        final int length = a.length;
+        byte[] consensusChars = new byte[length];
+        double[] consensusQuals = new double[length];
 
-        char[] consensusChars = new char[a.length()];
-        double[] consensusQuals = new double[a.length()];
-
-        for (int i=0; i < a.length(); i++) {
-            chA = a.charAt(i);
-            chB = b.charAt(i);
+        for (int i=0; i < length; i++) {
+            chA = a[i];
+            chB = b[i];
 
             if ((chA != chB) && (chA != wc) && (chB != wc))
                 return null;
@@ -228,12 +223,9 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
                 consensusChars[i] = chA;
                 consensusQuals[i] = haplotypeA.getQuals()[i]+haplotypeB.getQuals()[i];
             }
-
-
         }
 
-
-        return new Haplotype(new String(consensusChars), consensusQuals);
+        return new Haplotype(consensusChars, consensusQuals);
     }
     // calculate the haplotype scores by walking over all reads and comparing them to the haplotypes
     private double scoreReadsAgainstHaplotypes(List<Haplotype> haplotypes, ReadBackedPileup pileup, int contextSize) {
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java b/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
index 53a5b9bf5..c01596ae7 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
@@ -33,7 +33,6 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.util.Set;
 
 public class Haplotype {
     protected byte[] bases = null;
@@ -59,11 +58,6 @@ public class Haplotype {
         this.quals = quals;
     }
 
-    public Haplotype(String bases, double[] quals) {
-        this.bases = bases.getBytes();
-        this.quals = quals;
-    }
-
     public Haplotype(byte[] bases) {
         this(bases, 0);
     }
@@ -78,9 +72,6 @@ public class Haplotype {
         this.isReference = isRef;
     }
 
-
-    public String toString() { return new String(this.bases); }
-
     public double getQualitySum() {
         double s = 0;
         for (int k=0; k < bases.length; k++) {
@@ -104,7 +95,6 @@ public class Haplotype {
         return isReference;
     }
 
-
     public static List<Haplotype> makeHaplotypeListFromVariantContextAlleles(VariantContext vc, ReferenceContext ref, final int haplotypeSize) {