diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
index 983b77303..42bd8af9c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
@@ -301,7 +301,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
                     refBase = ref.getBase();
 
                     // Skip if this base is an 'N' or etc.
-                    if( BaseUtils.isRegularBase( (char)(bases[offset]) ) ) {
+                    if( BaseUtils.isRegularBase( bases[offset] ) ) {
 
                         // SOLID bams have inserted the reference base into the read if the color space in inconsistent with the read base so skip it
                         if( !gatkRead.getReadGroup().getPlatform().toUpperCase().contains("SOLID") || RAC.SOLID_RECAL_MODE.equalsIgnoreCase("DO_NOTHING") || !RecalDataManager.isInconsistentColorSpace( gatkRead, offset ) ) {
@@ -310,7 +310,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
                             updateDataFromRead( gatkRead, offset, refBase );
 
                         } else { // calculate SOLID reference insertion rate
-                            if( refBase == (char)bases[offset] ) {
+                            if( refBase == bases[offset] ) {
                                 solidInsertedReferenceBases++;
                             } else {
                                 otherColorSpaceInconsistency++;
diff --git a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 4c6932668..3b4154549 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -64,6 +64,7 @@ public class AlignmentUtils {
         return getMismatchCount(r, refSeq, refIndex).numMismatches;
     }
 
+    @Deprecated
     public static int numMismatches(SAMRecord r, String refSeq, int refIndex ) {
         if ( r.getReadUnmappedFlag() ) return 1000000;
         return numMismatches(r, StringUtil.stringToBytes(refSeq), refIndex);
@@ -73,11 +74,14 @@ public class AlignmentUtils {
         return getMismatchCount(r, refSeq, refIndex).mismatchQualities;
     }
 
+    @Deprecated
     public static long mismatchingQualities(SAMRecord r, String refSeq, int refIndex ) {
         if ( r.getReadUnmappedFlag() ) return 1000000;
         return numMismatches(r, StringUtil.stringToBytes(refSeq), refIndex);
      }
 
+    // todo -- this code and mismatchesInRefWindow should be combined and optimized into a single
+    // todo -- high performance implementation.  We can do a lot better than this right now
     private static MismatchCount getMismatchCount(SAMRecord r, byte[] refSeq, int refIndex) {
         MismatchCount mc = new MismatchCount();
 
@@ -188,9 +192,12 @@ public class AlignmentUtils {
                         if ( ignoreTargetSite && ref.getLocus().getStart() == currentPos )
                             continue;
 
-                        char readChr = (char)readBases[readIndex];
-                        if ( Character.toUpperCase(readChr) != Character.toUpperCase(refChr) )                       
+                        byte readChr = readBases[readIndex];
+                        if ( readChr != refChr )
                             sum += (qualitySumInsteadOfMismatchCount) ? readQualities[readIndex] : 1;
+//                        char readChr = (char)readBases[readIndex];
+//                        if ( Character.toUpperCase(readChr) != Character.toUpperCase(refChr) )
+//                            sum += (qualitySumInsteadOfMismatchCount) ? readQualities[readIndex] : 1;
                     }
                     break;
                 case I: