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 3bb6ee3f2..cd2c74273 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -274,12 +274,12 @@ public class RecalDataManager {
                     if( read.getReadNegativeStrandFlag() ) {
                         readBases = BaseUtils.simpleReverseComplement( read.getReadBases() );
                     }
-                    int[] inconsistency = new int[readBases.length];
+                    byte[] inconsistency = new byte[readBases.length];
                     int iii;
                     byte prevBase = (byte) colorSpace[0]; // The sentinel
                     for( iii = 0; iii < readBases.length; iii++ ) {
                         byte thisBase = (byte)getNextBaseFromColor( (char)prevBase, colorSpace[iii + 1] );
-                        inconsistency[iii] = ( thisBase == readBases[iii] ? 0 : 1 );
+                        inconsistency[iii] = (byte)( thisBase == readBases[iii] ? 0 : 1 );
                         prevBase = readBases[iii];
                     }
                     read.setAttribute( RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency );
@@ -469,7 +469,7 @@ public class RecalDataManager {
      */
     public static boolean isInconsistentColorSpace( final SAMRecord read, final int offset ) {
         if( read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) != null ) {
-            int[] colorSpace = ((int[])read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG));
+            byte[] colorSpace = ((byte[])read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG));
             return colorSpace[offset] != 0;
         } else {
             return false;
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java
index 08d1675fa..8d008d763 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java
@@ -9,7 +9,7 @@ public class IntervalCleanerIntegrationTest extends WalkerTest {
     @Test
     public void testIntervals() {
 
-        String[] md5lod5 = {"042c1c2649a51a260bc204ec5f256c1a", "460631e8d98644dcf53b3045ca40f02a"};
+        String[] md5lod5 = {"4a440cbb39a8093f28f6ce66d8b9a104", "460631e8d98644dcf53b3045ca40f02a"};
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 "-T IntervalCleaner -LOD 5 -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s",
                  2,