diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/Covariate.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/Covariate.java
index 809ab7e9a..486fb9651 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/Covariate.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/Covariate.java
@@ -33,13 +33,12 @@ import net.sf.samtools.SAMRecord;
  * Date: Oct 30, 2009
  *
  * The Covariate interface. A Covariate is a feature used in the recalibration that can be picked out of the read, offset, and corresponding reference bases
+ * In general most error checking and adjustments to the data are done before the call to the covariates getValue methods in order to speed up the code.
+ * This unfortunately muddies the code, but most of these corrections can be done per read while the covariates get called per base, resulting in a big speed up.
  */
 
 public interface Covariate {
-    public static final String COVARIATE_ERROR = "COVARIATE_ERROR";
-    public static final String COVARIATE_NULL = "COVARITATE_NULL";
-
-    public Comparable getValue(SAMRecord read, int offset, String readGroup, byte[] quals, char[] bases, char refBase); //used to pick out the value from attributes of the read
+    public Comparable getValue(SAMRecord read, int offset, String readGroup, byte[] quals, char[] bases, char refBase); // used to pick out the value from attributes of the read
 	public Comparable getValue(String str); // used to get value from input file
     public int estimatedNumberOfBins(); // used to estimate the amount space required for the HashMap
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java
index c715b0668..2969888b2 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java
@@ -242,14 +242,14 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
 		                    prevBase = bases[offset-1];
 		                    // Get the complement base strand if we are a negative strand read
 		                    if( read.getReadNegativeStrandFlag() ) {
-		                    	bases = BaseUtils.simpleComplement( read.getReadString() ).toCharArray();
+		                    	bases = BaseUtils.simpleComplement( read.getReadString() ).toCharArray(); // this is an expensive call
 		                        refBase = BaseUtils.simpleComplement( refBase );
 		                        prevBase = bases[offset+1];
 		                    }
 		                    
 		                    // skip if this base or the previous one was an 'N' or etc.
 		                    if( BaseUtils.isRegularBase(prevBase) && BaseUtils.isRegularBase(bases[offset]) ) {
-		                    	readGroup = read.getReadGroup().getReadGroupId();
+		                    	readGroup = read.getReadGroup().getReadGroupId(); // this is an expensive call
 		                    	updateDataFromRead( read, offset, readGroup, quals, bases, refBase );
 		                    }
                 		}
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CycleCovariate.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CycleCovariate.java
index 37b2bda00..1bc050172 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CycleCovariate.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CycleCovariate.java
@@ -47,7 +47,7 @@ public class CycleCovariate implements Covariate {
 	private String platform;
 
     public CycleCovariate() { // empty constructor is required to instantiate covariate in CovariateCounterWalker and TableRecalibrationWalker
-        platform = "SLX";
+        platform = "SLX"; // Solexa is the default
     }
 
     public CycleCovariate(final String _platform) {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/DinucCovariate.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/DinucCovariate.java
index f5a0d4ea1..34623c9ce 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/DinucCovariate.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/DinucCovariate.java
@@ -1,8 +1,6 @@
 package org.broadinstitute.sting.playground.gatk.walkers.Recalibration;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.Pair;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -34,9 +32,9 @@ import org.broadinstitute.sting.utils.Pair;
  * User: rpoplin
  * Date: Nov 3, 2009
  *
- * The Dinucleotide covariate. This base and the one that came before it in the read, remembering to swap directions on cardinality if negative strand read.
- * This covariate will return null if there are bases that don't belong such as 'N' or 'X'.
- * This covariate will also return null if attempting to get previous base at the start of the read.
+ * The Dinucleotide covariate. This base and the one that came before it in the read, remembering to swap directions if negative strand read.
+ * This covariate assumes that the bases have been swapped to their complement base counterpart if this is a negative strand read.
+ * This assumption is made to speed up the code.
  */
 
 public class DinucCovariate implements Covariate {