Add a comment to the method where the error appears

protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java

@@ -116,6 +116,10 @@ public class ReadCovariates {
     /**
      * Update the keys for mismatch, insertion, and deletion for the current covariate at read offset
      *
+     * NOTE: no checks are performed on the number of covariates, for performance reasons.  If the count increases
+     * after the keysCache has been accessed, this method will throw an ArrayIndexOutOfBoundsException.  This currently
+     * only occurs in the testing harness, and we don't anticipate that it will become a part of normal runs.
+     *
      * @param mismatch the mismatch key value
      * @param insertion the insertion key value
      * @param deletion the deletion key value