From 7f91b4d8242d8162ea852bd40aaba7a8d5a06627 Mon Sep 17 00:00:00 2001 From: asivache Date: Thu, 7 Jan 2010 21:30:55 +0000 Subject: [PATCH] Bug fix. It would be nice if we could extract ROD annotations for the whole length of an extended event (indel), and we tried... But alas, it does not work with the current ROD system (after extracting length on ref > 1 ROD data for a deletion, rod iterator crashes on the attempt to re-load annotations for next reference base) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2541 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/gatk/traversals/TraverseLoci.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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).