diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
index af981e676..ecaa15fe9 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
@@ -185,7 +185,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
      */
     private void writeActiveRegionsToStream( final ActiveRegionWalker<M,T> walker ) {
         // Just want to output the active regions to a file, not actually process them
-        for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion : workQueue ) {
+        for( final ActiveRegion activeRegion : workQueue ) {
             if( activeRegion.isActive ) {
                 walker.activeRegionOutStream.println( activeRegion.getLocation() );
             }
@@ -198,7 +198,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
         while( workQueue.peek() != null ) {
             final GenomeLoc extendedLoc = workQueue.peek().getExtendedLoc();
             if ( extendedLoc.getStop() < minStart || (currentContig != null && !workQueue.peek().getExtendedLoc().getContig().equals(currentContig))) {
-                final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion = workQueue.remove();
+                final ActiveRegion activeRegion = workQueue.remove();
                 sum = processActiveRegion( activeRegion, myReads, workQueue, sum, walker );
             } else {
                 break;
@@ -208,15 +208,15 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
         return sum;
     }
 
-    private T processActiveRegion( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final LinkedHashSet<GATKSAMRecord> reads, final Queue<org.broadinstitute.sting.utils.activeregion.ActiveRegion> workQueue, final T sum, final ActiveRegionWalker<M,T> walker ) {
+    private T processActiveRegion( final ActiveRegion activeRegion, final LinkedHashSet<GATKSAMRecord> reads, final Queue<ActiveRegion> workQueue, final T sum, final ActiveRegionWalker<M,T> walker ) {
         final ArrayList<GATKSAMRecord> placedReads = new ArrayList<GATKSAMRecord>();
         for( final GATKSAMRecord read : reads ) {
             final GenomeLoc readLoc = this.engine.getGenomeLocParser().createGenomeLoc( read );
             if( activeRegion.getLocation().overlapsP( readLoc ) ) {
                 // The region which the highest amount of overlap is chosen as the primary region for the read (tie breaking is done as right most region)
                 long maxOverlap = activeRegion.getLocation().sizeOfOverlap( readLoc );
-                org.broadinstitute.sting.utils.activeregion.ActiveRegion bestRegion = activeRegion;
-                for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion otherRegionToTest : workQueue ) {
+                ActiveRegion bestRegion = activeRegion;
+                for( final ActiveRegion otherRegionToTest : workQueue ) {
                     if( otherRegionToTest.getLocation().sizeOfOverlap(readLoc) >= maxOverlap ) {
                         maxOverlap = otherRegionToTest.getLocation().sizeOfOverlap( readLoc );
                         bestRegion = otherRegionToTest;
@@ -229,7 +229,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
                     if( !bestRegion.equals(activeRegion) ) {
                         activeRegion.add( read );
                     }
-                    for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion otherRegionToTest : workQueue ) {
+                    for( final ActiveRegion otherRegionToTest : workQueue ) {
                         if( !bestRegion.equals(otherRegionToTest) && otherRegionToTest.getExtendedLoc().overlapsP( readLoc ) ) {
                             otherRegionToTest.add( read );
                         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
index cbe791353..fed2c995e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
@@ -12,6 +12,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
 import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalSetRule;
@@ -77,7 +78,7 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
     public abstract ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context);
 
     // Map over the ActiveRegion
-    public abstract MapType map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker);
+    public abstract MapType map(final ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker);
 
     public final GenomeLocSortedSet extendIntervals( final GenomeLocSortedSet intervals, final GenomeLocParser genomeLocParser, IndexedFastaSequenceFile reference ) {
         final int activeRegionExtension = this.getClass().getAnnotation(ActiveRegionExtension.class).extension();