a little more doc

Author: tedsharpe

src/main/java/org/broadinstitute/hellbender/tools/AnalyzeSaturationMutagenesis.java

@@ -1018,10 +1018,11 @@ public CodonVariationGroup( final int[] refCodonValues, final CodonVariation cod
         // returns false if the presented variation cannot be added to the group
         public boolean addVariation( final CodonVariation codonVariation ) {
             final int codonId = codonVariation.getCodonId();
+            // if we're skipping a codon, start a new group (except for frameshift groups)
             if ( codonId > endingCodon + 1 && !isFrameShift ) return false;
             switch ( codonVariation.getVariationType() ) {
                 case FRAMESHIFT:
-                    return false;
+                    return false; // start new group for the frameshift
                 case INSERTION:
                     insCount += 1;
                     altCalls.append(codonTranslation.charAt(codonVariation.getCodonValue()));
@@ -1037,6 +1038,7 @@ public boolean addVariation( final CodonVariation codonVariation ) {
                             if ( !isEmpty() ) altCalls.append(aa);
                             break;
                         }
+                        // synonymous codon -- start new group
                         return false;
                     }
                     if ( isFrameShift && isEmpty() ) startingCodon = codonId;