diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java
index 712be5fba..b8633c401 100755
--- a/java/src/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java
@@ -27,12 +27,21 @@ public class PushbackIterator<T> implements Iterator<T>, Iterable<T> {
         return this;
     }
 
-    public T peek() {
+    /**
+     * Retrieves, but does not remove, the head of this iterator.
+     * @return T the next element in the iterator
+     * @throws NoSuchElementException - if the iterator doesn't have a next element
+     */
+    public T element() {
         T x = next();
         pushback(x);
         return x;
     }
 
+    /**
+     * @return the next element in the iteration.
+     * @throws NoSuchElementException - iteration has no more elements.
+     */
     public T next() {
         if (pushedElement != null) {
             final T ret = pushedElement;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRodIterator.java b/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRodIterator.java
index ea44e77a1..3aafcb69b 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRodIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRodIterator.java
@@ -34,8 +34,13 @@ public class IntervalRodIterator implements Iterator<IntervalRod> {
 		return iter.hasNext();
 	}
 
+    /**
+     * @return the next element in the iteration.
+     * @throws NoSuchElementException - iterator has no more elements.
+     */
 	@Override
 	public IntervalRod next() {
+        if (!this.hasNext()) throw new NoSuchElementException("IntervalRodIterator next called on iterator with no more elements");
         IntervalRod r = new IntervalRod(trackName, iter.next());
         //System.out.printf("IntervalRod next is %s%n", r);
         return r;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
index a74c6a468..56114d3e4 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
@@ -16,6 +16,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
+import java.util.NoSuchElementException;
 
 
 /**
@@ -349,8 +350,13 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
         return (mReader.hasNext());
     }
 
+    /**
+     * @return the next element in the iteration.
+     * @throws NoSuchElementException - iterator has no more elements.
+     */
     @Override
     public RodGLF next() {
+        if (!this.hasNext()) throw new NoSuchElementException("RodGLF next called on iterator with no more elements");
         mRecord = mReader.next();
         mLoc = GenomeLocParser.createGenomeLoc(mReader.getReferenceName(), mReader.getCurrentLocation(), mReader.getCurrentLocation());
         return this;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
index b6174fe98..b9cd653ff 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
@@ -12,6 +12,7 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.Iterator;
 import java.util.List;
+import java.util.NoSuchElementException;
 
 
 /**
@@ -282,7 +283,12 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         return mReader.hasNext();
     }
 
+    /**
+     * @return the next element in the iteration.
+     * @throws NoSuchElementException - iterator has no more elements.
+     */
     public RodVCF next() {
+        if (!this.hasNext()) throw new NoSuchElementException("RodVCF next called on iterator with no more elements");
         return new RodVCF(name, mReader.next(), mReader);
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java b/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java
index 686185811..60b4bd429 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java
@@ -584,8 +584,13 @@ public class SAMPileupRecord implements Genotype, GenotypeList {
 			return parser.hasNext();
 		}
 
+        /**
+         * @return the next element in the iteration.
+         * @throws NoSuchElementException - iterator has no more elements.
+         */
 		@Override
 		public SAMPileupRecord next() {
+             if (!this.hasNext()) throw new NoSuchElementException("SAMPileupRecord next called on iterator with no more elements");
 //			 if ( z == 0 ) t = System.currentTimeMillis();
 	          lastProcessedLine = parser.next();
 	          SAMPileupRecord n = new SAMPileupRecord(rodName);
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java b/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
index 8289acc21..232ef04c4 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
@@ -78,7 +78,8 @@ public class SeekableRODIterator<ROD extends ReferenceOrderedDatum> implements I
     public SeekableRODIterator(Iterator<ROD> it) {
         this.it = new PushbackIterator<ROD>(it);
         records = new LinkedList<ROD>();
-        ROD r = this.it.peek();
+        ROD r = null;
+        if (this.it.hasNext()) r = this.it.element();
         name = (r==null?null:r.getName());
     }
 
@@ -132,7 +133,7 @@ public class SeekableRODIterator<ROD extends ReferenceOrderedDatum> implements I
          // covered by new records, so we need to load them too:
 
          while ( it.hasNext() ) {
-             ROD r = it.peek();
+             ROD r = it.element();
              if ( r == null ) {
                  it.next();
                  continue;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java
index 64bf552df..87e6836f1 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java
@@ -78,8 +78,12 @@ public class rodGELI extends BasicReferenceOrderedDatum {
 		public boolean hasNext() {
 			return iterator.hasNext();
 		}
-
+        /**
+         * @return the next element in the iteration.
+         * @throws NoSuchElementException - iterator has no more elements.
+         */
 		public rodGELI next() {
+            if (!this.hasNext()) throw new NoSuchElementException("RodGELI next called on iterator with no more elements");
             return new rodGELI(rodName, iterator.next());
 		}
 
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodPicardDbSNP.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodPicardDbSNP.java
index 20e8258ef..a259da718 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodPicardDbSNP.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodPicardDbSNP.java
@@ -31,10 +31,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Collections;
-import java.util.Arrays;
+import java.util.*;
 
 /**
  * @author alecw@broadinstitute.org
@@ -270,7 +267,12 @@ public class rodPicardDbSNP implements VariationRod {
             return reader.hasNext();
         }
 
+        /**
+         * @return the next element in the iteration.
+         * @throws NoSuchElementException - iterator has no more elements.
+         */
         public rodPicardDbSNP next() {
+            if (!this.hasNext()) throw new NoSuchElementException("rodPicardDbSNP next called on iterator with no more elements");
             return new rodPicardDbSNP(reader.next());
         }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java
index 917cec9be..33723c165 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java
@@ -113,9 +113,13 @@ public class rodSAMPileup extends BasicReferenceOrderedDatum implements Genotype
 			return parser.hasNext();
 		}
 
+        /**
+         * @return the next element in the iteration.
+         * @throws NoSuchElementException - iterator has no more elements.
+         */
 		@Override
 		public rodSAMPileup next() {
-
+            if (!this.hasNext()) throw new NoSuchElementException("rodSAMPileup next called on iterator with no more elements");
 			rodSAMPileup result = new rodSAMPileup(rodName);
 			
 			SAMPileupRecord r = parser.next();