diff --git a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
index de8c81031..673b1524d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
@@ -436,6 +436,18 @@ public class BaseUtils {
         return mostFrequentBaseIndex;
     }
 
+    static public int mostFrequentBaseIndexNotRef(int[] baseCounts, int refBaseIndex) {
+        int tmp = baseCounts[refBaseIndex];
+        baseCounts[refBaseIndex] = -1;
+        int result = mostFrequentBaseIndex(baseCounts);
+        baseCounts[refBaseIndex] = tmp;
+        return result;
+    }
+
+    static public int mostFrequentBaseIndexNotRef(int[] baseCounts, byte refSimpleBase) {
+        return mostFrequentBaseIndexNotRef(baseCounts, simpleBaseToBaseIndex(refSimpleBase));
+    }
+
     /**
      * Returns the most common base in the basecounts array. To be used with pileup.getBaseCounts.
      *
diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 9bd3f603c..a0b970dbc 100755
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -360,6 +360,23 @@ public class MathUtils {
         return Math.pow(10,log10MultinomialProbability(n, k, log10P));
     }
 
+    /**
+     * calculate the Root Mean Square of an array of integers
+     * @param x  an byte[] of numbers
+     * @return   the RMS of the specified numbers.
+    */
+    public static double rms(byte[] x) {
+        if ( x.length == 0 )
+            return 0.0;
+
+        double rms = 0.0;
+        for (int i : x)
+            rms += i * i;
+        rms /= x.length;
+        return Math.sqrt(rms);
+    }
+
+
     /**
      * calculate the Root Mean Square of an array of integers
      * @param x  an int[] of numbers
@@ -1074,6 +1091,11 @@ public class MathUtils {
         return ((-q)/10.0);
     }
 
+    /**
+     * Returns the phred scaled value of probability p
+     * @param p probability (between 0 and 1).
+     * @return phred scaled probability of p
+     */
     public static byte probabilityToPhredScale (double p) {
         return (byte) ((-10) * Math.log10(p));
     }