diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index 5fe8ed7a1..5d92c5c2d 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
@@ -203,7 +203,7 @@ public abstract class TraversalEngine {
 
 
     public boolean hasLocations() {
-        return this.locs != null;
+        return this.locs != null && !this.locs.isEmpty();
     }
 
     // --------------------------------------------------------------------------------------------------------------
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
index 9b0d630ba..35c95098a 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
@@ -34,7 +34,8 @@ public class TraverseByLoci extends TraversalEngine {
         super(reads, ref, rods);
     }
 
-    public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) {
+    @Override
+    public <M,T> T traverse(Walker<M,T> walker, List<GenomeLoc> locations) {
         if ( walker instanceof LocusWalker ) {
             LocusWalker<M, T> locusWalker = (LocusWalker<M, T>)walker;
             T sum = traverseByLoci(locusWalker, locations);
@@ -54,7 +55,7 @@ public class TraverseByLoci extends TraversalEngine {
      * @param <T>    ReduceType -- the result of calling reduce() on the walker
      * @return 0 on success
      */
-    protected <M, T> T traverseByLoci(LocusWalker<M, T> walker, ArrayList<GenomeLoc> locations) {
+    protected <M, T> T traverseByLoci(LocusWalker<M, T> walker, List<GenomeLoc> locations) {
         logger.debug("Entering traverseByLoci");
 
         if(readsFiles.size() > 1)
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLocusWindows.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLocusWindows.java
index 1e9d86b2f..9bf39ec29 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLocusWindows.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLocusWindows.java
@@ -32,7 +32,8 @@ public class TraverseByLocusWindows extends TraversalEngine {
         super(reads, ref, rods);
     }
 
-    public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) {
+    @Override
+    public <M,T> T traverse(Walker<M,T> walker, List<GenomeLoc> locations) {
         if ( walker instanceof LocusWindowWalker ) {
             LocusWindowWalker<M, T> locusWindowWalker = (LocusWindowWalker<M, T>)walker;
             T sum = traverseByIntervals(locusWindowWalker, locations);
@@ -52,7 +53,7 @@ public class TraverseByLocusWindows extends TraversalEngine {
      * @param <T>    ReduceType -- the result of calling reduce() on the walker
      * @return 0 on success
      */
-    protected <M, T> T traverseByIntervals(LocusWindowWalker<M, T> walker, ArrayList<GenomeLoc> locations) {
+    protected <M, T> T traverseByIntervals(LocusWindowWalker<M, T> walker, List<GenomeLoc> locations) {
         logger.debug("Entering traverseByIntervals");
 
         if(readsFiles.size() > 1)
@@ -83,7 +84,7 @@ public class TraverseByLocusWindows extends TraversalEngine {
         return sum;
     }
 
-    protected <M, T> T strictIntervalTraversal(LocusWindowWalker<M, T> walker, ArrayList<GenomeLoc> locations, T sum) {
+    protected <M, T> T strictIntervalTraversal(LocusWindowWalker<M, T> walker, List<GenomeLoc> locations, T sum) {
         for ( GenomeLoc interval : locations ) {
             logger.debug(String.format("Processing interval %s", interval.toString()));
 
@@ -98,7 +99,7 @@ public class TraverseByLocusWindows extends TraversalEngine {
         return sum;
     }
 
-    protected <M, T> T fullInputTraversal(LocusWindowWalker<M, T> walker, ArrayList<GenomeLoc> locations, T sum) {
+    protected <M, T> T fullInputTraversal(LocusWindowWalker<M, T> walker, List<GenomeLoc> locations, T sum) {
 
         // set everything up
         GenomeLoc currentInterval = (locations.size() > 0 ? locations.get(0) : null);
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
index 876507ba2..a66b6fc48 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
@@ -32,7 +32,8 @@ public class TraverseByReads extends TraversalEngine {
         super(reads, ref, rods);        
     }
 
-    public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) {
+    @Override
+    public <M,T> T traverse(Walker<M,T> walker, List<GenomeLoc> locations) {
         if ( walker instanceof ReadWalker ) {
             Walker x = walker;
             ReadWalker<?, ?> readWalker = (ReadWalker<?, ?>)x;
@@ -53,7 +54,7 @@ public class TraverseByReads extends TraversalEngine {
      * @param <>    ReduceType -- the result of calling reduce() on the walker
      * @return 0 on success
      */
-    public <M, T> Object traverseByRead(ReadWalker<M, T> walker, ArrayList<GenomeLoc> locations) {
+    public <M, T> Object traverseByRead(ReadWalker<M, T> walker, List<GenomeLoc> locations) {
         samReadIter = initializeReads();
         if ( refFileName != null && !locations.isEmpty() )
             GenomeLoc.setupRefContigOrdering(new FastaSequenceFile2(refFileName));
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReference.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReference.java
index 8964b4fea..1f4e7729e 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReference.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReference.java
@@ -42,7 +42,7 @@ public class TraverseByReference extends TraverseByLoci {
      * @param <T>    ReduceType -- the result of calling reduce() on the walker
      * @return 0 on success
      */
-    protected <M, T> T traverseByLoci(LocusWalker<M, T> walker, ArrayList<GenomeLoc> locations) {
+    protected <M, T> T traverseByLoci(LocusWalker<M, T> walker, List<GenomeLoc> locations) {
         logger.debug("Entering traverseByReference");
 
         // initialize the walker object
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
index c0e195cb7..f45021c37 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
@@ -256,7 +256,8 @@ public class TraverseDuplicates extends TraversalEngine {
     // old style interface to the system
     //
     // --------------------------------------------------------------------------------------------------------------
-    public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) {
+    @Override
+    public <M,T> T traverse(Walker<M,T> walker, List<GenomeLoc> locations) {
         if ( walker instanceof DuplicateWalker) {
             Walker x = walker;
             DuplicateWalker<?, ?> dupWalker = (DuplicateWalker<?, ?>)x;
@@ -269,7 +270,7 @@ public class TraverseDuplicates extends TraversalEngine {
     /**
      * Should we deleted at the soonist possible opportunity
      */
-    public <M, T> Object traverseByRead(DuplicateWalker<M, T> walker, ArrayList<GenomeLoc> locations) {
+    public <M, T> Object traverseByRead(DuplicateWalker<M, T> walker, List<GenomeLoc> locations) {
         samReadIter = initializeReads();
 
         // Initialize the walker
diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index 6bed69ea5..672583179 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -275,7 +275,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
      * @param curr Current genome Location
      * @return true if we are past the last location to process
      */
-    public static boolean pastFinalLocation(GenomeLoc curr, ArrayList<GenomeLoc> locs) {
+    public static boolean pastFinalLocation(GenomeLoc curr, List<GenomeLoc> locs) {
         return (locs.size() > 0 && curr.isPast(locs.get(locs.size() - 1)));
     }