diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java index b4b6ab67a..87dd0f04f 100644 --- a/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java @@ -95,7 +95,7 @@ public class ReferenceContext { * Get the base at the given locus. * @return The base at the given locus from the reference. */ - public int getSimpleBase() { + public int getBaseIndex() { return BaseUtils.simpleBaseToBaseIndex(getBase()); }