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 3449baafd..9eebf9223 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 = "v2.2.2"; // Major version, minor version, and build number
+    private static final String versionString = "v2.2.3"; // 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)
@@ -311,7 +311,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
      * @param context The AlignmentContext which holds the reads covered by this locus
      * @param ref The reference base
      */
-    private static void updateMismatchCounts(Pair<Long, Long> counts, AlignmentContext context, char ref) {
+    private static void updateMismatchCounts(final Pair<Long, Long> counts, final AlignmentContext context, final char ref) {
         for( PileupElement p : context.getPileup() ) {
             final char readChar = (char)(p.getBase());
             final int readCharBaseIndex = BaseUtils.simpleBaseToBaseIndex(readChar);
@@ -377,7 +377,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
         final long curMismatches = datum.getNumMismatches();
 
         // Add one to the number of observations and potentially one to the number of mismatches
-        datum.increment( (char)base, (char)refBase ); // Dangerous: If you don't cast to char than the bytes default to the (long, long) version of the increment method which is really bad
+        datum.increment( (char)base, (char)refBase ); // Dangerous: If you don't cast to char then the bytes default to the (long, long) version of the increment method which is really bad
         countedBases++;
         novel_counts.second++;
         novel_counts.first += datum.getNumMismatches() - curMismatches; // For sanity check to ensure novel mismatch rate vs dnsnp mismatch rate is reasonable
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 7e1f60c2a..07cd9a175 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -260,11 +260,11 @@ public class RecalDataManager {
                     if( read.getReadNegativeStrandFlag() ) {
                         readBases = BaseUtils.simpleReverseComplement( read.getReadBases() );
                     }
-                    byte[] inconsistency = new byte[readBases.length];
+                    final 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] );
+                        final byte thisBase = (byte)getNextBaseFromColor( (char)prevBase, colorSpace[iii + 1] );
                         inconsistency[iii] = (byte)( thisBase == readBases[iii] ? 0 : 1 );
                         prevBase = readBases[iii];
                     }
@@ -289,9 +289,9 @@ public class RecalDataManager {
      * @param refBases The reference for this read
      * @return A new array of quality scores that have been ref bias corrected
      */
-    public static byte[] calcColorSpace( SAMRecord read, byte[] originalQualScores, final String SOLID_RECAL_MODE, final Random coinFlip, final char[] refBases ) {
+    public static byte[] calcColorSpace( final SAMRecord read, byte[] originalQualScores, final String SOLID_RECAL_MODE, final Random coinFlip, final char[] refBases ) {
 
-        Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG);
+        final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG);
         if( attr != null ) {
             char[] colorSpace;
             if( attr instanceof String ) {
@@ -308,16 +308,16 @@ public class RecalDataManager {
                 readBases = BaseUtils.simpleReverseComplement( read.getReadBases() );
                 refBasesDirRead = BaseUtils.simpleReverseComplement( refBases );
             }
-            int[] inconsistency = new int[readBases.length];
+            final int[] inconsistency = new int[readBases.length];
             byte prevBase = (byte) colorSpace[0]; // The sentinel
             for( int iii = 0; iii < readBases.length; iii++ ) {
-                byte thisBase = (byte)getNextBaseFromColor( (char)prevBase, colorSpace[iii + 1] );
+                final byte thisBase = (byte)getNextBaseFromColor( (char)prevBase, colorSpace[iii + 1] );
                 colorImpliedBases[iii] = thisBase;
                 inconsistency[iii] = ( thisBase == readBases[iii] ? 0 : 1 );
                 prevBase = readBases[iii];
             }
 
-            boolean isMappedToReference = (refBases != null && refBases.length == inconsistency.length);
+            final boolean isMappedToReference = (refBases != null && refBases.length == inconsistency.length);
 
             // 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
@@ -328,7 +328,7 @@ public class RecalDataManager {
                 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);
-            }
+            } 
 
         } else if ( !warnUserNoColorSpace ) { // Warn the user if we can't find the color space tag
             Utils.warnUser("Unable to find color space information in SOLID read. First observed at read with name = " + read.getReadName());
@@ -350,27 +350,26 @@ public class RecalDataManager {
      * @param setBaseN Should we also set the base to N as well as quality zero in order to visualize in IGV or something similar
      * @return The byte array of original quality scores some of which might have been set to zero
      */
-    private static byte[] solidRecalSetToQZero( SAMRecord read, byte[] readBases, int[] inconsistency, byte[] originalQualScores,
+    private static byte[] solidRecalSetToQZero( final SAMRecord read, byte[] readBases, final int[] inconsistency, final byte[] originalQualScores,
                                                 final char[] refBases, final boolean isMappedToRef, final boolean setBaseN ) {
 
+        final boolean negStrand = read.getReadNegativeStrandFlag();
         for( int iii = 1; iii < originalQualScores.length - 1; iii++ ) {
             if( inconsistency[iii] == 1 ) {
                 if( !isMappedToRef || (char)readBases[iii] == refBases[iii] ) {
-                    originalQualScores[iii] = (byte)0;
+                    if( negStrand ) { originalQualScores[originalQualScores.length-(iii+1)] = (byte)0; }
+                    else { originalQualScores[iii] = (byte)0; }
                     if( setBaseN ) { readBases[iii] = (byte)'N'; }
                 }
                 // Set the prev base to Q0 as well
                 if( !isMappedToRef || (char)readBases[iii-1] == refBases[iii-1] ) {
-                    originalQualScores[iii-1] = (byte)0;
+                    if( negStrand ) { originalQualScores[originalQualScores.length-iii] = (byte)0; }
+                    else { originalQualScores[iii-1] = (byte)0; }
                     if( setBaseN ) { readBases[iii-1] = (byte)'N'; }
                 }
-                //if( !isMappedToRef || (char)readBases[iii+1] == refBases[iii+1] ) {
-                //    originalQualScores[iii+1] = (byte)0;
-                //    if( setBaseN ) { readBases[iii+1] = (byte)'N'; }
-                //}
             }
         }
-        if( read.getReadNegativeStrandFlag() ) {
+        if( negStrand ) {
             readBases = BaseUtils.simpleReverseComplement( readBases.clone() ); // Put the bases back in reverse order to stuff them back in the read
         }
         read.setReadBases( readBases );
@@ -387,10 +386,10 @@ public class RecalDataManager {
      * @param isMappedToRef Is this read mapped fully to a reference
      * @param coinFlip A random number generator
      */
-    private static void solidRecalRemoveRefBias( SAMRecord read, byte[] readBases, int[] inconsistency, byte[] colorImpliedBases,
-                                                 final char[] refBases, final boolean isMappedToRef, final Random coinFlip ) {
+    private static void solidRecalRemoveRefBias( final SAMRecord read, byte[] readBases, final int[] inconsistency, final byte[] colorImpliedBases,
+                                                 final char[] refBases, final boolean isMappedToRef, final Random coinFlip) {
 
-        Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_QUAL_ATTRIBUTE_TAG);
+        final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_QUAL_ATTRIBUTE_TAG);
         if( attr != null ) {
             byte[] colorSpaceQuals;
             if( attr instanceof String ) {
@@ -402,27 +401,32 @@ public class RecalDataManager {
             for( int iii = 1; iii < inconsistency.length - 1; iii++ ) {
                 if( inconsistency[iii] == 1 ) {
                     for( int jjj = iii - 1; jjj <= iii; jjj++ ) { // Correct this base and the one before it along the direction of the read
-                        if( !isMappedToRef || (char)readBases[jjj] == refBases[jjj] ) {
-                            if( colorSpaceQuals[jjj] == colorSpaceQuals[jjj+1] ) { // Equal evidence for the color implied base and the reference base, so flip a coin
-                                int rand = coinFlip.nextInt( 2 );
-                                if( rand == 0 ) { // The color implied base won the coin flip
-                                    readBases[jjj] = colorImpliedBases[jjj];
-                                }
-                            } else {
-                                int maxQuality = Math.max((int)colorSpaceQuals[jjj], (int)colorSpaceQuals[jjj+1]);
-                                int minQuality = Math.min((int)colorSpaceQuals[jjj], (int)colorSpaceQuals[jjj+1]);
-                                int diffInQuality = maxQuality - minQuality;
-                                int numLow = minQuality;
-                                if( numLow == 0 ) { numLow = 1; }
-                                int numHigh = Math.round( numLow * (float)Math.pow(10.0f, (float) diffInQuality / 10.0f) ); // The color with higher quality is exponentially more likely
-                                int rand = coinFlip.nextInt( numLow + numHigh );
-                                if( rand >= numLow ) {
-                                    if( maxQuality == (int)colorSpaceQuals[jjj] ) {
+                        if( jjj == iii || inconsistency[jjj] == 0 ) { // Don't want to correct the previous base a second time if it was already corrected in the previous step
+                            if( !isMappedToRef || (char)readBases[jjj] == refBases[jjj] ) {
+                                if( colorSpaceQuals[jjj] == colorSpaceQuals[jjj+1] ) { // Equal evidence for the color implied base and the reference base, so flip a coin
+                                    final int rand = coinFlip.nextInt( 2 );
+                                    if( rand == 0 ) { // The color implied base won the coin flip
                                         readBases[jjj] = colorImpliedBases[jjj];
                                     }
                                 } else {
-                                    if( minQuality == (int)colorSpaceQuals[jjj] ) {
-                                        readBases[jjj] = colorImpliedBases[jjj];
+                                    final int maxQuality = Math.max((int)colorSpaceQuals[jjj], (int)colorSpaceQuals[jjj+1]);
+                                    final int minQuality = Math.min((int)colorSpaceQuals[jjj], (int)colorSpaceQuals[jjj+1]);
+                                    int diffInQuality = maxQuality - minQuality;
+                                    int numLow = minQuality;
+                                    if( numLow == 0 ) {
+                                        numLow++;
+                                        diffInQuality++;
+                                    }
+                                    final int numHigh = Math.round( numLow * (float)Math.pow(10.0f, (float) diffInQuality / 10.0f) ); // The color with higher quality is exponentially more likely
+                                    final int rand = coinFlip.nextInt( numLow + numHigh );
+                                    if( rand >= numLow ) { // higher q score won
+                                        if( maxQuality == (int)colorSpaceQuals[jjj] ) {
+                                            readBases[jjj] = colorImpliedBases[jjj];
+                                        } // else ref color had higher q score, and won out, so nothing to do here
+                                    } else { // lower q score won
+                                        if( minQuality == (int)colorSpaceQuals[jjj] ) {
+                                            readBases[jjj] = colorImpliedBases[jjj];
+                                        } // else ref color had lower q score, and won out, so nothing to do here
                                     }
                                 }
                             }
@@ -457,7 +461,7 @@ public class RecalDataManager {
             case '3': // simple complement
                 return BaseUtils.simpleComplement( prevBase );
             default:
-                throw new StingException( "Unrecognized color space in SOLID bam, color = " + color );
+                throw new StingException( "Unrecognized color space in SOLID read, color = " + color );
         }
     }
 
@@ -468,9 +472,9 @@ public class RecalDataManager {
      * @return Returns true if the base is inconsistent with the color space
      */
     public static boolean isInconsistentColorSpace( final SAMRecord read, final int offset ) {
-        Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG);
+        final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG);
         if( attr != null ) {
-            byte[] colorSpace = (byte[])attr;
+            final byte[] colorSpace = (byte[])attr;
             return colorSpace[offset] != 0;
         } else {
             return false;
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 bd709e2fe..eb1d649fc 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 = "v2.2.5"; // Major version, minor version, and build number
+    private static final String versionString = "v2.2.6"; // Major version, minor version, and build number
     private SAMFileWriter OUTPUT_BAM = null;// The File Writer that will write out the recalibrated bam
     private Random coinFlip; // Random number generator is used to remove reference bias in solid bams
     private static final long RANDOM_SEED = 1032861495;
@@ -175,7 +175,6 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
                                 throw new StingException( "Malformed input recalibration file. The requested covariate type (" + (vals[iii] + "Covariate") + ") isn't a valid covariate option." );
                             }
                         }
-
                     }
 
                 } else { // Found a line of data
@@ -259,7 +258,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
      * For each covariate read in a value and parse it. Associate those values with the data itself (num observation and num mismatches)
      * @param line A line of CSV data read from the recalibration table data file
      */
-    private void addCSVData(String line) {
+    private void addCSVData(final String line) {
         final String[] vals = line.split(",");
 
         // Check if the data line is malformed, for example if the read group string contains a comma then it won't be parsed correctly
@@ -302,7 +301,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         byte[] originalQuals = read.getBaseQualities();
         final byte[] recalQuals = originalQuals.clone();
 
-        String platform = read.getReadGroup().getPlatform();
+        final String platform = read.getReadGroup().getPlatform();
         if( platform.equalsIgnoreCase("SOLID") && !RAC.SOLID_RECAL_MODE.equalsIgnoreCase("DO_NOTHING") ) {
             originalQuals = RecalDataManager.calcColorSpace( read, originalQuals, RAC.SOLID_RECAL_MODE, coinFlip, refBases );
         }
@@ -351,7 +350,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
      * @param key The list of Comparables that were calculated from the covariates
      * @return A recalibrated quality score as a byte
      */
-    private byte performSequentialQualityCalculation(Object... key ) {
+    private byte performSequentialQualityCalculation(final Object... key ) {
 
         final byte qualFromRead = (byte)Integer.parseInt(key[1].toString());
         final Object[] readGroupCollapsedKey = new Object[1];
@@ -413,7 +412,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
      * @param originalQuals The list of original base quality scores
      * @param recalQuals A list of the new recalibrated quality scores
      */
-    private void preserveQScores( final byte[] originalQuals, byte[] recalQuals ) {
+    private void preserveQScores( final byte[] originalQuals, final byte[] recalQuals ) {
         for( int iii = 0; iii < recalQuals.length; iii++ ) {
             if( originalQuals[iii] < PRESERVE_QSCORES_LESS_THAN ) {
                 recalQuals[iii] = originalQuals[iii];
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 36201dc26..427da8ff9 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -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", "27b3eaf3c02ffc5fb3d7815468d9958e");
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "0f4a882d78747380af2822317c7b6045");
         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", "a39afc94ed74f8137c9d43285997bd90" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "41b0313bfcaf5afb3cb85f9830e79769" );
 
         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", "bf8d62beda7d3cf38d660d7939901192" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "8120b648a43b293b84a7cb6374513fb8" );
 
         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", "ad345fcfb2faaf97eb0291ffa61b3228" );
+        e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "d9d29f38f8ea31ac267f9d937cad9291" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();