diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
index 7addb2746..5b1c1fb7d 100644
--- a/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
@@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.contexts;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
+import net.sf.samtools.util.StringUtil;
 
 /**
  * The section of the reference that overlaps with the given
@@ -38,6 +39,8 @@ import org.broadinstitute.sting.utils.BaseUtils;
  */
 
 public class ReferenceContext {
+    final public static boolean UPPERCASE_REFERENCE = true;
+
     /**
      * The locus.
      */
@@ -64,7 +67,7 @@ public class ReferenceContext {
      * @param base reference base at that locus.
      */
     public ReferenceContext( GenomeLoc locus, byte base ) {
-        this( locus, locus, new byte[] { base } );
+        this( locus, locus, new byte[] { UPPERCASE_REFERENCE ? StringUtil.toUpperCase(base) : base } );
     }
 
     // todo -- this really should take the referenceview as an option and only grab the bases if necessary
@@ -75,6 +78,8 @@ public class ReferenceContext {
         this.locus = locus;
         this.window = window;
         this.bases = bases;
+
+        if (UPPERCASE_REFERENCE) StringUtil.toUpperCase(bases);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
index 304c75800..04650cea5 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -34,6 +34,7 @@ import java.util.*;
 
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMUtils;
 
 /**
  * Created by IntelliJ IDEA.
@@ -428,7 +429,9 @@ public class RecalDataManager {
         if( attr != null ) {
             byte[] colorSpaceQuals;
             if( attr instanceof String ) {
-                colorSpaceQuals = QualityUtils.fastqToPhred((String)attr);
+                String x = (String)attr;
+                colorSpaceQuals = x.getBytes();
+                SAMUtils.fastqToPhred(colorSpaceQuals);
             } else {
                 throw new StingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_QUAL_ATTRIBUTE_TAG, read.getReadName()));
             }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index e5f518d2a..9d743d781 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -34,11 +34,7 @@ import java.util.Random;
 import java.util.ResourceBundle;
 import java.util.regex.Pattern;
 
-import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMFileWriter;
-import net.sf.samtools.SAMProgramRecord;
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMTag;
+import net.sf.samtools.*;
 import net.sf.samtools.util.SequenceUtil;
 
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
@@ -57,6 +53,7 @@ import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
@@ -359,7 +356,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
         read.setBaseQualities( recalQuals ); // Overwrite old qualities with new recalibrated qualities
         if ( read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG) == null ) { // Save the old qualities if the tag isn't already taken in the read
-            read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, QualityUtils.phredToFastq(originalQuals));
+            read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, SAMUtils.phredToFastq(originalQuals));
         }
 
         if (read.getAttribute(SAMTag.UQ.name()) != null) {
diff --git a/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/java/src/org/broadinstitute/sting/utils/BaseUtils.java
index 975a8c112..cdbda9a6a 100644
--- a/java/src/org/broadinstitute/sting/utils/BaseUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/BaseUtils.java
@@ -64,7 +64,7 @@ public class BaseUtils {
         return t;
     }
 
-    public static boolean isTransition( byte  base1, byte  base2 ) {
+    public static boolean isTransition( byte base1, byte  base2 ) {
         int b1 = simpleBaseToBaseIndex(base1);
         int b2 = simpleBaseToBaseIndex(base2);
         return b1 == 0 && b2 == 2 || b1 == 2 && b2 == 0 ||
@@ -144,6 +144,7 @@ public class BaseUtils {
         }
         return bases;
     }
+
     /**
      * Converts a simple base to a base index
      *
diff --git a/java/src/org/broadinstitute/sting/utils/QualityUtils.java b/java/src/org/broadinstitute/sting/utils/QualityUtils.java
index 1a728a8a9..827b5916a 100755
--- a/java/src/org/broadinstitute/sting/utils/QualityUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/QualityUtils.java
@@ -217,73 +217,4 @@ public class QualityUtils {
     static public byte[] reverseQualityArray( byte[] quals ) {
         return BaseUtils.reverse(quals); // no sense in duplicating functionality
     }
-
-    // TODO --
-    // TODO --
-    // TODO -- stolen from SAMUtils in picard -- remove when public access is granted
-    // TODO --
-    // TODO --
-
-    /**
-     * Convert an array of bytes, in which each byte is a binary phred quality score, to
-     * printable ASCII representation of the quality scores, ala FASTQ format.
-     * @param buffer Array of bytes in which each byte is a binar phred score.
-     * @param offset Where in buffer to start conversion.
-     * @param length How many bytes of buffer to convert.
-     * @return String with ASCII representation of those quality scores.
-     */
-    public static String phredToFastq(final byte[] buffer, final int offset, final int length) {
-        final char[] chars = new char[length];
-        for (int i = 0; i < length; i++) {
-            chars[i] = phredToFastq(buffer[offset+i] & 0xFF);
-        }
-        return new String(chars);
-    }
-
-    /** convenience -- should be pushed back into Picard */
-    public static String phredToFastq(final byte[] buffer) {
-        return phredToFastq(buffer, 0, buffer.length);
-    }
-
-    /**
-     * Convert a single binary phred score to printable ASCII representation, ala FASTQ format.
-     * @param phredScore binary phred score.
-     * @return Printable ASCII representation of phred score.
-     */
-    public static char phredToFastq(final int phredScore) {
-        if (phredScore < 0 || phredScore > MAX_QUAL_SCORE) {
-            throw new IllegalArgumentException("Cannot encode phred score: " + phredScore);
-        }
-        return (char) (33 + phredScore);
-    }
-
-    /**
-     * Convert a string with phred scores in printable ASCII FASTQ format to an array
-     * of binary phred scores.
-     * @param fastq Phred scores in FASTQ printable ASCII format.
-     * @return byte array of binary phred scores in which each byte corresponds to a character in the input string.
-     */
-    public static byte[] fastqToPhred(final String fastq) {
-        if (fastq == null) {
-            return null;
-        }
-        final int length = fastq.length();
-        final byte[] scores = new byte[length];
-        for (int i = 0; i < length; i++) {
-            scores[i] = (byte) fastqToPhred(fastq.charAt(i));
-        }
-        return scores;
-    }
-
-    /**
-     * Convert a single printable ASCII FASTQ format phred score to binary phred score.
-     * @param ch Printable ASCII FASTQ format phred score.
-     * @return Binary phred score.
-     */
-    public static int fastqToPhred(final char ch) {
-        if (ch < 33 || ch > 126) {
-            throw new IllegalArgumentException("Invalid fastq character: " + ch);
-        }
-        return (ch - 33);
-    }
 }
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java
index ea5ca09ff..609f3c5a0 100755
--- a/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java
@@ -104,7 +104,7 @@ public class LocusReferenceViewUnitTest extends ReferenceViewTemplate {
             GenomeLoc locus = shardIterator.next();
 
             ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(locus.getContig(), locus.getStart(), locus.getStop());
-            char expected = StringUtil.bytesToString(expectedAsSeq.getBases()).charAt(0);
+            char expected = Character.toUpperCase(StringUtil.bytesToString(expectedAsSeq.getBases()).charAt(0));
             char actual = view.getReferenceContext(locus).getBaseAsChar();
 
             Assert.assertEquals(String.format("Value of base at position %s in shard %s does not match expected", locus.toString(), shard.getGenomeLocs()),