diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index dbffacfbc..c18eef23f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -287,6 +287,11 @@ public final class GenomeLocParser {
         return new GenomeLoc(contig, index, start, stop);
     }
 
+    public GenomeLoc createGenomeLocOnContig(final String contig, final int start, final int stop) {
+        GenomeLoc contigLoc = createOverEntireContig(contig);
+        return new GenomeLoc(contig, getContigIndex(contig), start, stop).intersect(contigLoc);
+    }
+
     /**
      * validate a position or interval on the genome as valid
      *
diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
index 0d12d53cc..c12dfcee9 100644
--- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
+++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
@@ -31,7 +31,7 @@ public class ActiveRegion implements HasGenomeLocation {
         this.isActive = isActive;
         this.genomeLocParser = genomeLocParser;
         this.extension = extension;
-        extendedLoc = genomeLocParser.createGenomeLoc(activeRegionLoc.getContig(), activeRegionLoc.getStart() - extension, activeRegionLoc.getStop() + extension);
+        extendedLoc = genomeLocParser.createGenomeLocOnContig(activeRegionLoc.getContig(), activeRegionLoc.getStart() - extension, activeRegionLoc.getStop() + extension);
         fullExtentReferenceLoc = extendedLoc;
     }