diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java index 4bfc85bae..0d546eec9 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java @@ -81,7 +81,7 @@ public class TraverseLoci extends TraversalEngine { } // Iterate forward to get all reference ordered data covering this location - final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(location); + final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(locus.getLocation()); // create reference context. Note that if we have a pileup of "extended events", the context will // hold the (longest) stretch of deleted reference bases (if deletions are present in the pileup).