diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusContextProvider.java b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusContextProvider.java
index d1afab694..2de7c65a7 100755
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusContextProvider.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusContextProvider.java
@@ -1,13 +1,11 @@
 package org.broadinstitute.sting.gatk.dataSources.providers;
 
 import edu.mit.broad.picard.filter.FilteringIterator;
-import edu.mit.broad.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.iterators.LocusIterator;
-import org.broadinstitute.sting.gatk.iterators.LocusIteratorByHanger;
-import org.broadinstitute.sting.gatk.traversals.TraversalStatistics;
+import org.broadinstitute.sting.gatk.iterators.LocusContextIterator;
+import org.broadinstitute.sting.gatk.iterators.LocusContextIteratorByHanger;
 import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
@@ -26,14 +24,14 @@ public class LocusContextProvider {
 
     // What's the last locus accessed?  Used for sanity checking.
     private GenomeLoc lastLoc = null;
-    private LocusIterator loci;
+    private LocusContextIterator loci;
     private LocusContext locus;
     protected static Logger logger = Logger.getLogger(LocusContextProvider.class);
 
     public LocusContextProvider( Iterator<SAMRecord> reads ) {
         this.reads = new FilteringIterator(reads, new TraversalEngine.locusStreamFilterFunc());
         // prepare the iterator by loci from reads
-        loci = new LocusIteratorByHanger(this.reads);
+        loci = new LocusContextIteratorByHanger(this.reads);
     }
 
     public LocusContext getLocusContext( GenomeLoc loc ) {
@@ -56,7 +54,7 @@ public class LocusContextProvider {
         return locusContext;
     }
 
-    private LocusContext advanceReadsToLoc(LocusIterator locusIter, GenomeLoc target) {
+    private LocusContext advanceReadsToLoc(LocusContextIterator locusIter, GenomeLoc target) {
         if ( ! locusIter.hasNext() )
             return null;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/LocusContextIterator.java
similarity index 89%
rename from java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java
rename to java/src/org/broadinstitute/sting/gatk/iterators/LocusContextIterator.java
index 34920bb3b..bc20f1c79 100755
--- a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/LocusContextIterator.java
@@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
 /**
  * Iterator that traverses a SAM File, accumulating information on a per-locus basis
  */
-public abstract class LocusIterator implements Iterable<LocusContext>, CloseableIterator<LocusContext> {
+public abstract class LocusContextIterator implements Iterable<LocusContext>, CloseableIterator<LocusContext> {
     // -----------------------------------------------------------------------------------------------------------------
     //
     // constructors and other basic operations
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java b/java/src/org/broadinstitute/sting/gatk/iterators/LocusContextIteratorByHanger.java
similarity index 93%
rename from java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java
rename to java/src/org/broadinstitute/sting/gatk/iterators/LocusContextIteratorByHanger.java
index a8d10f93d..0995e7691 100755
--- a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/LocusContextIteratorByHanger.java
@@ -1,29 +1,24 @@
 package org.broadinstitute.sting.gatk.iterators;
 
-import net.sf.samtools.util.CloseableIterator;
-import net.sf.samtools.util.RuntimeIOException;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.AlignmentBlock;
 import org.broadinstitute.sting.utils.*;
 
-import java.util.List;
 import java.util.Iterator;
 
 import org.broadinstitute.sting.utils.RefHanger;
-import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
-import org.broadinstitute.sting.gatk.iterators.LocusIterator;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.apache.log4j.Logger;
 
 /**
  * Iterator that traverses a SAM File, accumulating information on a per-locus basis
  */
-public class LocusIteratorByHanger extends LocusIterator {
+public class LocusContextIteratorByHanger extends LocusContextIterator {
 
     /**
      * our log, which we want to capture anything from this class
      */
-    private static Logger logger = Logger.getLogger(LocusIteratorByHanger.class);
+    private static Logger logger = Logger.getLogger(LocusContextIteratorByHanger.class);
 
     // -----------------------------------------------------------------------------------------------------------------
     //
@@ -43,7 +38,7 @@ public class LocusIteratorByHanger extends LocusIterator {
     // constructors and other basic operations
     //
     // -----------------------------------------------------------------------------------------------------------------
-    public LocusIteratorByHanger(final Iterator<SAMRecord> samIterator) {
+    public LocusContextIteratorByHanger(final Iterator<SAMRecord> samIterator) {
         this.it = new PushbackIterator<SAMRecord>(samIterator);
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
index 35c95098a..1c819c899 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
@@ -7,14 +7,13 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
-import org.broadinstitute.sting.gatk.iterators.LocusIterator;
-import org.broadinstitute.sting.gatk.iterators.LocusIteratorByHanger;
+import org.broadinstitute.sting.gatk.iterators.LocusContextIterator;
+import org.broadinstitute.sting.gatk.iterators.LocusContextIteratorByHanger;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
 
 import java.util.List;
 import java.util.Iterator;
-import java.util.ArrayList;
 import java.io.File;
 
 import net.sf.samtools.SAMRecord;
@@ -109,7 +108,7 @@ public class TraverseByLoci extends TraversalEngine {
         FilteringIterator filterIter = new FilteringIterator(readIter, new locusStreamFilterFunc());
 
         boolean done = false;
-        LocusIterator iter = new LocusIteratorByHanger(filterIter);
+        LocusContextIterator iter = new LocusContextIteratorByHanger(filterIter);
         while (iter.hasNext() && !done) {
             TraversalStatistics.nRecords++;
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/iterators/SingleLocusIterator.java b/java/src/org/broadinstitute/sting/playground/gatk/iterators/SingleLocusContextIterator.java
similarity index 94%
rename from java/src/org/broadinstitute/sting/playground/gatk/iterators/SingleLocusIterator.java
rename to java/src/org/broadinstitute/sting/playground/gatk/iterators/SingleLocusContextIterator.java
index 0300ba1af..bb7eda734 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/iterators/SingleLocusIterator.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/iterators/SingleLocusContextIterator.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.playground.gatk.iterators;
 import net.sf.samtools.util.CloseableIterator;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
-import org.broadinstitute.sting.gatk.iterators.LocusIterator;
+import org.broadinstitute.sting.gatk.iterators.LocusContextIterator;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.Predicate;
@@ -19,7 +19,7 @@ import edu.mit.broad.picard.filter.FilteringIterator;
 /**
  * Iterator that traverses a SAM File, accumulating information on a per-locus basis
  */
-public class SingleLocusIterator extends LocusIterator {
+public class SingleLocusContextIterator extends LocusContextIterator {
 
     // -----------------------------------------------------------------------------------------------------------------
     //
@@ -37,7 +37,7 @@ public class SingleLocusIterator extends LocusIterator {
     // constructors and other basic operations
     //
     // -----------------------------------------------------------------------------------------------------------------
-    public SingleLocusIterator(final CloseableIterator<SAMRecord> samIterator) {
+    public SingleLocusContextIterator(final CloseableIterator<SAMRecord> samIterator) {
         FilteringIterator filterIter = new FilteringIterator(samIterator, new locusStreamFilterFunc());
         this.it = new PushbackIterator<SAMRecord>(filterIter);
 
@@ -105,7 +105,7 @@ public class SingleLocusIterator extends LocusIterator {
                     read.getReferenceName().equals(contig); // should be index for efficiency
         }
     }
-    Predicate KeepReadP = new SingleLocusIterator.KeepReadPFunc();
+    Predicate KeepReadP = new SingleLocusContextIterator.KeepReadPFunc();
 
     private void calcOffsetsOfWindow(final int position) {
         offsets.clear();