diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index 174e810c2..e04f5bc4b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -170,9 +170,9 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     /////////////////////////////
     private RecalDataManager dataManager; // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps
     private final ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // List of covariates to be used in this calculation
-    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,.*");
+    public static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
+    public static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
+    public static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
     public static final String EOF_MARKER = "EOF";
     private long numReadsWithMalformedColorSpace = 0;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 25f0d0fe2..d1e9a236f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -888,9 +888,20 @@ public class ReadUtils {
                     if (endsWithinCigar)
                         fallsInsideDeletion = cigarElement.getOperator() == CigarOperator.DELETION;
 
-                    // if we end outside the current cigar element, we need to check if the next element is a deletion.
+                    // if we end outside the current cigar element, we need to check if the next element is an insertion or deletion.
                     else {
                         nextCigarElement = cigarElementIterator.next();
+
+                        // if it's an insertion, we need to clip the whole insertion before looking at the next element
+                        if (nextCigarElement.getOperator() == CigarOperator.INSERTION) {
+                            readBases += nextCigarElement.getLength();
+                            if (!cigarElementIterator.hasNext())
+                                throw new ReviewedStingException("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- call Mauricio");
+
+                            nextCigarElement = cigarElementIterator.next();
+                        }
+
+                        // if it's a deletion, we will pass the information on to be handled downstream.
                         fallsInsideDeletion = nextCigarElement.getOperator() == CigarOperator.DELETION;
                     }