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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
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asivache 2010-01-07 21:30:55 +00:00
parent 5f58492401
commit 7f91b4d824
1 changed files with 1 additions and 1 deletions
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java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
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@ -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).