From c8a5007c85988db81f3980c5def5ef3593aa1632 Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Fri, 14 Feb 2014 11:40:22 -0500 Subject: [PATCH] Add a comment to the method where the error appears --- .../sting/utils/recalibration/ReadCovariates.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java index 9ef94b8e8..6efed2689 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java +++ b/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