diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReferenceIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReferenceIterator.java
deleted file mode 100644
index 59fc02093..000000000
--- a/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReferenceIterator.java
+++ /dev/null
@@ -1,81 +0,0 @@
-package org.broadinstitute.sting.gatk.iterators;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
-
-import java.util.Iterator;
-
-import net.sf.picard.reference.ReferenceSequence;
-import net.sf.samtools.util.StringUtil;
-
-/**
- *
- * User: aaron
- * Date: Apr 2, 2009
- * Time: 2:12:12 PM
- *
- * The Broad Institute
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT 
- * This software and its documentation are copyright 2009 by the
- * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- *
- * This software is supplied without any warranty or guaranteed support whatsoever. Neither
- * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
- *
- */
-
-
-/**
- * @author aaron
- * @version 1.0
- * @date Apr 2, 2009
- * <p/>
- * Class BoundedReferenceIterator
- * <p/>
- * This class is a decorator class from Reference Iterator (though it is constrained
- * by the fact that referenceIterator.seekForwardOffset explicitly returns a referenceIterator
- * for now).
- * <p/>
- * TODO: Fix the underlying iterator and this class to model a real decorator pattern
- */
-public class BoundedReferenceIterator implements Iterator<Character> {
-    private ReferenceSequence referenceSequence = null;
-
-    // The start and end point of the read relative to the chromosome.
-    private long start;
-    private long end;
-
-    // 0-based index into the base array.
-    private int position;
-    // the location to screen over
-
-    /**
-     * Default constructor
-     *
-     * @param referenceSequenceFile sequence file over which to iterate
-     * @param loc subsequence of the reference over which to iterate.
-     */
-    public BoundedReferenceIterator(IndexedFastaSequenceFile referenceSequenceFile, GenomeLoc loc) {
-        start = loc.getStart();
-        end = loc.getStop();
-        position = 0;
-
-        referenceSequence = referenceSequenceFile.getSubsequenceAt( loc.getContig(), position, end );
-    }
-
-
-    // our adapted next function
-    public boolean hasNext() {
-        return (start + position) > end;
-    }
-
-    public Character next() {
-        return StringUtil.bytesToString( referenceSequence.getBases(), position++, 1 ).charAt(0);
-    }
-
-    public void remove() {
-        throw new UnsupportedOperationException("Cannot remove from a reference iterator");
-    }
-
-
-}