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 9eebf9223..b814db015 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
@@ -103,7 +103,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
     private long solidInsertedReferenceBases = 0; // Number of bases where we believe SOLID has inserted the reference because the color space is inconsistent with the read base
     private long otherColorSpaceInconsistency = 0; // Number of bases where the color space is inconsistent with the read but the reference wasn't inserted.
     private int numUnprocessed = 0; // Number of consecutive loci skipped because we are only processing every Nth site
-    private static final String versionString = "v2.2.3"; // Major version, minor version, and build number
+    private static final String versionString = "v2.2.4"; // Major version, minor version, and build number
     private Pair<Long, Long> dbSNP_counts = new Pair<Long, Long>(0L, 0L);  // mismatch/base counts for dbSNP loci
     private Pair<Long, Long> novel_counts = new Pair<Long, Long>(0L, 0L);  // mismatch/base counts for non-dbSNP loci
     private static final double DBSNP_VS_NOVEL_MISMATCH_RATE = 2.0;        // rate at which dbSNP sites (on an individual level) mismatch relative to novel sites (determined by looking at NA12878)
@@ -170,7 +170,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
         if( USE_STANDARD_COVARIATES ) {
             for( Class<?> covClass : standardClasses ) {
                 try {
-                    Covariate covariate = (Covariate)covClass.newInstance();
+                    final Covariate covariate = (Covariate)covClass.newInstance();
                     requestedCovariates.add( covariate );
                 } catch ( InstantiationException e ) {
                     throw new StingException( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
@@ -189,7 +189,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
                         if( !requiredClasses.contains( covClass ) && (!USE_STANDARD_COVARIATES || !standardClasses.contains( covClass )) ) {
                             try {
                                 // Now that we've found a matching class, try to instantiate it
-                                Covariate covariate = (Covariate)covClass.newInstance();
+                                final Covariate covariate = (Covariate)covClass.newInstance();
                                 requestedCovariates.add( covariate );
                             } catch ( InstantiationException e ) {
                                 throw new StingException( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
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 07cd9a175..c8ea00bd1 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -45,10 +45,10 @@ import net.sf.samtools.SAMReadGroupRecord;
 
 public class RecalDataManager {
     
-    public NestedHashMap data; // The full dataset
-    private NestedHashMap dataCollapsedReadGroup; // Table where everything except read group has been collapsed
-    private NestedHashMap dataCollapsedQualityScore; // Table where everything except read group and quality score has been collapsed
-    private ArrayList<NestedHashMap> dataCollapsedByCovariate; // Tables where everything except read group, quality score, and given covariate has been collapsed
+    public final NestedHashMap data; // The full dataset
+    private final NestedHashMap dataCollapsedReadGroup; // Table where everything except read group has been collapsed
+    private final NestedHashMap dataCollapsedQualityScore; // Table where everything except read group and quality score has been collapsed
+    private final ArrayList<NestedHashMap> dataCollapsedByCovariate; // Tables where everything except read group, quality score, and given covariate has been collapsed
 
     public final static String ORIGINAL_QUAL_ATTRIBUTE_TAG = "OQ"; // The tag that holds the original quality scores
     public final static String COLOR_SPACE_QUAL_ATTRIBUTE_TAG = "CQ"; // The tag that holds the color space quality scores for SOLID bams
@@ -59,10 +59,14 @@ public class RecalDataManager {
 
     RecalDataManager() {
     	data = new NestedHashMap();
+        dataCollapsedReadGroup = null;
+        dataCollapsedQualityScore = null;
+        dataCollapsedByCovariate = null;
     }
 
     RecalDataManager( final boolean createCollapsedTables, final int numCovariates ) {
     	if( createCollapsedTables ) { // Initialize all the collapsed tables, only used by TableRecalibrationWalker
+            data = null;
             dataCollapsedReadGroup = new NestedHashMap();
             dataCollapsedQualityScore = new NestedHashMap();
             dataCollapsedByCovariate = new ArrayList<NestedHashMap>();
@@ -71,6 +75,9 @@ public class RecalDataManager {
             }
         } else {
             data = new NestedHashMap();
+            dataCollapsedReadGroup = null;
+            dataCollapsedQualityScore = null;
+            dataCollapsedByCovariate = null;
         }            
     }
     
@@ -321,10 +328,10 @@ public class RecalDataManager {
 
             // Now that we have the inconsistency array apply the desired correction to the inconsistent bases
             if( SOLID_RECAL_MODE.equalsIgnoreCase("SET_Q_ZERO") ) { // Set inconsistent bases and the one before it to Q0
-                boolean setBaseN = false;
+                final boolean setBaseN = false;
                 originalQualScores = solidRecalSetToQZero(read, readBases, inconsistency, originalQualScores, refBasesDirRead, isMappedToReference, setBaseN);
             } else if( SOLID_RECAL_MODE.equalsIgnoreCase("SET_Q_ZERO_BASE_N") ) {
-                boolean setBaseN = true;
+                final boolean setBaseN = true;
                 originalQualScores = solidRecalSetToQZero(read, readBases, inconsistency, originalQualScores, refBasesDirRead, isMappedToReference, setBaseN);
             } else if( SOLID_RECAL_MODE.equalsIgnoreCase("REMOVE_REF_BIAS") ) { // Use the color space quality to probabilistically remove ref bases at inconsistent color space bases
                 solidRecalRemoveRefBias(read, readBases, inconsistency, colorImpliedBases, refBasesDirRead, isMappedToReference, coinFlip);
@@ -469,13 +476,33 @@ public class RecalDataManager {
      * Check if this base is inconsistent with its color space. If it is then SOLID inserted the reference here and we should reduce the quality
      * @param read The read which contains the color space to check against
      * @param offset The offset in the read at which to check
-     * @return Returns true if the base is inconsistent with the color space
+     * @return Returns true if the base was inconsistent with the color space
      */
     public static boolean isInconsistentColorSpace( final SAMRecord read, final int offset ) {
         final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG);
         if( attr != null ) {
-            final byte[] colorSpace = (byte[])attr;
-            return colorSpace[offset] != 0;
+            final byte[] inconsistency = (byte[])attr;
+            // NOTE: The inconsistency array is in the direction of the read, not aligned to the reference!
+            if( read.getReadNegativeStrandFlag() ) { // Negative direction
+                return inconsistency[inconsistency.length - offset - 1] != 0;
+            } else { // Forward direction
+                return inconsistency[offset] != 0;
+            }
+
+            // This block of code is if you want to check both the offset and the next base for color space inconsistency
+            //if( read.getReadNegativeStrandFlag() ) { // Negative direction
+            //    if( offset == 0 ) {
+            //        return inconsistency[0] != 0;
+            //    } else {
+            //        return (inconsistency[inconsistency.length - offset - 1] != 0) || (inconsistency[inconsistency.length - offset] != 0);
+            //    }
+            //} else { // Forward direction
+            //    if( offset == inconsistency.length - 1 ) {
+            //        return inconsistency[inconsistency.length - 1] != 0;
+            //    } else {
+            //        return (inconsistency[offset] != 0) || (inconsistency[offset + 1] != 0);
+            //    }
+            //}
         } else {
             return false;
         }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
index 6e307b705..ecc07afec 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
@@ -63,7 +63,7 @@ public class RecalibrationArgumentCollection {
     public boolean EXCEPTION_IF_NO_TILE = false;
 
     
-    public boolean checkSolidRecalMode() {
+    public final boolean checkSolidRecalMode() {
         return ( SOLID_RECAL_MODE.equalsIgnoreCase("DO_NOTHING") || SOLID_RECAL_MODE.equalsIgnoreCase("SET_Q_ZERO") ||
                  SOLID_RECAL_MODE.equalsIgnoreCase("SET_Q_ZERO_BASE_N") || SOLID_RECAL_MODE.equalsIgnoreCase("REMOVE_REF_BIAS") );
     }
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 16bcdd2a3..40adfeab4 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -94,7 +94,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
     private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
     private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
-    private static final String versionString = "v2.2.6"; // Major version, minor version, and build number
+    private static final String versionString = "v2.2.7"; // Major version, minor version, and build number
     private Random coinFlip; // Random number generator is used to remove reference bias in solid bams
     private static final long RANDOM_SEED = 1032861495;
 
@@ -120,7 +120,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         }
 
         // Get a list of all available covariates
-        List<Class<? extends Covariate>> classes = PackageUtils.getClassesImplementingInterface(Covariate.class);
+        final List<Class<? extends Covariate>> classes = PackageUtils.getClassesImplementingInterface(Covariate.class);
 
         int lineNumber = 0;
         boolean foundAllCovariates = false;
@@ -223,7 +223,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         // Take the header of the input SAM file and tweak it by adding in a new programRecord with the version number and list of covariates that were used
         final SAMFileHeader header = getToolkit().getSAMFileHeader().clone();
         if( !NO_PG_TAG ) {
-            SAMProgramRecord programRecord = new SAMProgramRecord( "GATK TableRecalibration" );
+            final SAMProgramRecord programRecord = new SAMProgramRecord( "GATK TableRecalibration" );
             programRecord.setProgramVersion( versionString );
             String commandLineString = "Covariates used = [";
             for( Covariate cov : requestedCovariates ) {
@@ -232,10 +232,10 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
             commandLineString = commandLineString.substring(0, commandLineString.length() - 2); // trim off the trailing comma
             commandLineString += "] ";
             // Add all of the arguments from the recalibraiton argument collection to the command line string
-            Field[] fields = RAC.getClass().getFields();
+            final Field[] fields = RAC.getClass().getFields();
             for( Field field : fields ) {
-                ArgumentTypeDescriptor atd = ArgumentTypeDescriptor.create(field.getType());
-                List<ArgumentDefinition> adList = atd.createArgumentDefinitions(new ArgumentSource(field.getType(), field));
+                final ArgumentTypeDescriptor atd = ArgumentTypeDescriptor.create(field.getType());
+                final List<ArgumentDefinition> adList = atd.createArgumentDefinitions(new ArgumentSource(field.getType(), field));
                 for( ArgumentDefinition ad : adList ) {
                     commandLineString += (ad.fullName + "=" + JVMUtils.getFieldValue(field, RAC) + ", ");
                 }
@@ -355,8 +355,8 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         final RecalDatum globalRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(0).get( readGroupCollapsedKey ));
         double globalDeltaQ = 0.0;
         if( globalRecalDatum != null ) {
-            double globalDeltaQEmpirical = globalRecalDatum.getEmpiricalQuality();
-            double aggregrateQReported = globalRecalDatum.getEstimatedQReported();
+            final double globalDeltaQEmpirical = globalRecalDatum.getEmpiricalQuality();
+            final double aggregrateQReported = globalRecalDatum.getEstimatedQReported();
             globalDeltaQ = globalDeltaQEmpirical - aggregrateQReported;
         }
 
@@ -366,7 +366,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         final RecalDatum qReportedRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(1).get( qualityScoreCollapsedKey ));
         double deltaQReported = 0.0;
         if( qReportedRecalDatum != null ) {
-            double deltaQReportedEmpirical = qReportedRecalDatum.getEmpiricalQuality();
+            final double deltaQReportedEmpirical = qReportedRecalDatum.getEmpiricalQuality();
             deltaQReported = deltaQReportedEmpirical - qualFromRead - globalDeltaQ;
         }
         
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index 427da8ff9..09c4ce095 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -17,9 +17,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     public void testCountCovariates1() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "e5b2d5a2f4283718dae678cbc84be847" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "ff1b3a18b67b09560cacc3b5dea0a034");
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "89084b43b824f9e3c5e2afdfe0930542");
         e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "7d6428a76e07ed4b99351aa4df89634d" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "a93b0263acdc856b885f95848852140d" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "6ede6fc840c4e5070a58a919b48e7504" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -50,9 +50,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     public void testTableRecalibrator1() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "6c59d291c37d053e0f188b762f3060a5" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "0f4a882d78747380af2822317c7b6045");
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "e06f1397b9c40f75e96cd3df76730ee0");
         e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "7ebdce416b72679e1cf88cc9886a5edc" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "41b0313bfcaf5afb3cb85f9830e79769" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "48ddc93cae054f9423f3a7ed9f36540e" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -80,7 +80,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testTableRecalibratorMaxQ70() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "8120b648a43b293b84a7cb6374513fb8" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "665711dfb81d67582b28faea24e26160" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -109,7 +109,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesVCF() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "d90342547ed228cf446caf594586f4b0");
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "9b9d21ffb70f15ef2aebad21f3fc05cb");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -136,7 +136,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesNoReadGroups() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "7e3045dcb2da1f4b305db7fa72bd1b51" );
+        e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "a86c64f649b847b7f81ac50a808d3d45" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -165,7 +165,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testTableRecalibratorNoReadGroups() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "d9d29f38f8ea31ac267f9d937cad9291" );
+        e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "32ad300e8c094ed2c1ec6c531180fe70" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();