diff --git a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
index fad2320fc..093da7dd6 100755
--- a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
@@ -9,14 +9,17 @@ import net.sf.samtools.SAMUtils;
  * @author Kiran Garimella
  */
 public class QualityUtils {
-
     public final static byte MAX_QUAL_SCORE = SAMUtils.MAX_PHRED_SCORE;
     public final static double MIN_REASONABLE_ERROR = 0.0001;
     public final static byte MAX_REASONABLE_Q_SCORE = 40;
     public final static byte MIN_USABLE_Q_SCORE = 6;
-
     public final static int MAPPING_QUALITY_UNAVAILABLE = 255;
 
+    private static double qualToErrorProbCache[] = new double[256];
+    static {
+        for (byte i = 0; i < 256; i++) qualToErrorProbCache[i] = qualToErrorProbRaw(i);
+    }
+
     /**
      * Private constructor.  No instantiating this class!
      */
@@ -33,10 +36,6 @@ public class QualityUtils {
         return 1.0 - qualToErrorProb(qual);
     }
 
-    static public double qualToProb(int qual) {
-        return qualToProb( (double)qual );
-    }
-
     static public double qualToProb(double qual) {
         return 1.0 - Math.pow(10.0, qual/(-10.0));
     }
@@ -48,10 +47,14 @@ public class QualityUtils {
      * @param qual a quality score (0-40)
      * @return a probability (0.0-1.0)
      */
-    static public double qualToErrorProb(byte qual) {
+    static public double qualToErrorProbRaw(byte qual) {
         return Math.pow(10.0, ((double) qual)/-10.0);
     }
 
+    static public double qualToErrorProb(byte qual) {
+        return qualToErrorProbCache[qual];
+    }
+
     /**
      * Convert a probability to a quality score.  Note, this is capped at Q40.
      *
@@ -110,88 +113,4 @@ public class QualityUtils {
         //return (byte) Math.min(qual, maxQual);
         return (byte) Math.max(Math.min(qual, maxQual), 1);
     }
-
-    /**
-     * Compress a base and a probability into a single byte so that it can be output in a SAMRecord's SQ field.
-     * Note: the highest probability this function can encode is 64%, so this function should only never be used on the best base hypothesis.
-     * Another note: the probability encoded here gets rounded to the nearest 1%.
-     *
-     * @param baseIndex the base index
-     * @param prob      the base probability
-     * @return a byte containing the index and the probability
-     */
-    static public byte baseAndProbToCompressedQuality(int baseIndex, double prob) {
-        byte compressedQual = 0;
-
-        compressedQual = (byte) baseIndex;
-
-        byte cprob = (byte) (100.0*prob);
-        byte qualmask = (byte) 252;
-        compressedQual += ((cprob << 2) & qualmask);
-        
-        return compressedQual;
-    }
-
-    /**
-     * From a compressed base, extract the base index (0:A, 1:C, 2:G, 3:T)
-     *
-     * @param compressedQual the compressed quality score, as returned by baseAndProbToCompressedQuality
-     * @return base index
-     */
-    static public int compressedQualityToBaseIndex(byte compressedQual) {
-        return (int) (compressedQual & 0x3);
-    }
-
-    /**
-     * From a compressed base, extract the base probability
-     *
-     * @param compressedQual the compressed quality score, as returned by baseAndProbToCompressedQuality
-     * @return the probability
-     */
-    static public double compressedQualityToProb(byte compressedQual) {
-        // Because java natives are signed, extra care must be taken to avoid
-        // shifting a 1 into the sign bit in the implicit promotion of 2 to an int.
-        int x2 = ((int) compressedQual) & 0xff;
-        x2 = (x2 >>> 2);
-
-        return ((double) x2)/100.0;
-    }
-
-    /**
-     * Return the complement of a compressed quality
-     *
-     * @param compressedQual  the compressed quality score (as returned by baseAndProbToCompressedQuality)
-     * @return the complementary compressed quality
-     */
-    static public byte complementCompressedQuality(byte compressedQual) {
-        int baseIndex = compressedQualityToBaseIndex(compressedQual);
-        double prob = compressedQualityToProb(compressedQual);
-
-        return baseAndProbToCompressedQuality(BaseUtils.complementIndex(baseIndex), prob);
-    }
-
-    /**
-     * Return the reverse complement of a byte array of compressed qualities
-     *
-     * @param compressedQuals  a byte array of compressed quality scores
-     * @return the reverse complement of the byte array
-     */
-    static public byte[] reverseComplementCompressedQualityArray(byte[] compressedQuals) {
-        byte[] rcCompressedQuals = new byte[compressedQuals.length];
-
-        for (int pos = 0; pos < compressedQuals.length; pos++) {
-            rcCompressedQuals[compressedQuals.length - pos - 1] = complementCompressedQuality(compressedQuals[pos]);
-        }
-
-        return rcCompressedQuals;
-    }
-
-    /**
-     * Return the reverse of a byte array of qualities (compressed or otherwise)
-     * @param quals   the array of bytes to be reversed
-     * @return the reverse of the quality array
-     */
-    static public byte[] reverseQualityArray( byte[] quals ) {
-        return Utils.reverse(quals); // no sense in duplicating functionality
-    }
 }