diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/DataSource.java b/java/src/org/broadinstitute/sting/gatk/dataSources/DataSource.java
deleted file mode 100644
index 47c67c7e8..000000000
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/DataSource.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package org.broadinstitute.sting.gatk.dataSources;
-
-import org.broadinstitute.sting.gatk.dataSources.shards.DataShard;
-
-/**
- * User: aaron
- * Date: Mar 25, 2009
- * Time: 6:20:00 PM
- * <p/>
- * 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.
- * <p/>
- * 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.
- */
-public interface DataSource {
-
-    public DataShard toChunk(int chunkCount);
-}
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/DataSourceBuilder.java b/java/src/org/broadinstitute/sting/gatk/dataSources/DataSourceBuilder.java
deleted file mode 100644
index ecbf23584..000000000
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/DataSourceBuilder.java
+++ /dev/null
@@ -1,74 +0,0 @@
-package org.broadinstitute.sting.gatk.dataSources;
-
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-
-import java.util.ArrayList;
-import java.io.File;
-
-/**
- * User: aaron
- * Date: Mar 25, 2009
- * Time: 4:51:39 PM
- * <p/>
- * 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.
- * <p/>
- * 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.
- */
-public class DataSourceBuilder {
-
-    // storage for the passed file
-    ArrayList<File> passFiles = new ArrayList<File>();
-
-    public DataSourceBuilder() {
-
-    }
-
-    /**
-     * add a file used to generate the data sources
-     *
-     * @param fileName the filename that should be used
-     */
-    public void addDataFile(String fileName) {
-        // for now, just add it to the internal file list
-        passFiles.add(new File(fileName));
-    }
-
-    /**
-     * add a file used to generate the data sources
-     *
-     * @param file the filename that should be used
-     */
-    public void addDataFile(File file) {
-        // for now, just add it to the internal file list
-        passFiles.add(file);
-    }
-
-    public DataSource build(Walker inputWalker) {
-        if (inputWalker instanceof ReadWalker) {
-
-        }
-
-        return null;
-    }
-
-
-    /**
-     * this section contains the private methods to create data sources
-     * based on the type of walker we're passed in.
-     */
-
-
-    /**
-     * we know we have a read data source, let's get the 
-     * @return
-     */
-    //private ReadDataSource generateReadDataSource() {
-        // 
-    //}
-
-}
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/datum/Datum.java b/java/src/org/broadinstitute/sting/gatk/dataSources/datum/Datum.java
deleted file mode 100644
index 6609e830a..000000000
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/datum/Datum.java
+++ /dev/null
@@ -1,35 +0,0 @@
-package org.broadinstitute.sting.gatk.dataSources.datum;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
-
-import java.io.Serializable;
-/**
- *
- * User: aaron
- * Date: Mar 30, 2009
- * Time: 1:32:34 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 Mar 30, 2009
- * <p/>
- * interface Datum
- * <p/>
- * The interface for all Datum Types.
- */
-public interface Datum extends Serializable {
-
-    // this function is used for tracking where we are in a genome
-    public GenomeLoc getSequenceLocation();
-}
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/datum/LocusDatum.java b/java/src/org/broadinstitute/sting/gatk/dataSources/datum/LocusDatum.java
deleted file mode 100644
index 1ab986732..000000000
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/datum/LocusDatum.java
+++ /dev/null
@@ -1,94 +0,0 @@
-package org.broadinstitute.sting.gatk.dataSources.datum;
-
-import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.utils.GenomeLoc;
-
-import java.util.List;
-
-/**
- *
- * User: aaron
- * Date: Mar 30, 2009
- * Time: 3:08:28 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 Mar 30, 2009
- * <p/>
- * Class LocusDatum
- * <p/>
- * The datum for loci.  It contains the reference base, locusContext,
- * and the reference order data.
- */
-public class LocusDatum implements Datum {
-
-    // our reference order data    
-    private final List<ReferenceOrderedDatum> rodData;
-    // our seq base
-    private final char ref;
-    // our locus context  
-    private final LocusContext context;
-
-    /**
-     * the locus dataum constructor
-     *
-     * @param rodData our reference data
-     * @param ref     our reference sequence base position
-     * @param context the genome context we're in
-     */
-    public LocusDatum(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
-        this.rodData = rodData;
-        this.ref = ref;
-        this.context = context;
-    }
-
-    /**
-     * return the Reference order data for this position
-     *
-     * @return
-     */
-    public List<ReferenceOrderedDatum> getRodData() {
-        return rodData;
-    }
-
-    /**
-     * return the reference base
-     *
-     * @return a character representing the reference base
-     */
-    public char getRef() {
-        return ref;
-    }
-
-    /**
-     * get the locus context at the current position
-     *
-     * @return
-     */
-    public LocusContext getContext() {
-        return context;
-    }
-
-    /**
-     * gets the current postion in the sequence, which comes
-     * free from underlying data types
-     *
-     * @return our current GenomeLocation
-     */
-    public GenomeLoc getSequenceLocation() {
-        return this.context.getLocation();
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/datum/ReadDatum.java b/java/src/org/broadinstitute/sting/gatk/dataSources/datum/ReadDatum.java
deleted file mode 100644
index e45babdb7..000000000
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/datum/ReadDatum.java
+++ /dev/null
@@ -1,65 +0,0 @@
-package org.broadinstitute.sting.gatk.dataSources.datum;
-
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
-/**
- *
- * User: aaron
- * Date: Mar 30, 2009
- * Time: 2:53:37 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 Mar 30, 2009
- * <p/>
- * Class ReadDatum
- * <p/>
- * The base read datum class.
- */
-public class ReadDatum implements Datum {
-
-    // our SAM record
-    final private SAMRecord sam;
-
-    // our locus context
-    final private LocusContext locus;
-
-    // the constructor, taking a sam read and a locus
-    public ReadDatum(SAMRecord r, LocusContext locus) {
-        this.sam = r;
-        this.locus = locus;
-    }
-
-    // get the SAMRecord
-    public SAMRecord getRead() {
-        return this.sam;
-    }
-
-    // get the locus context
-    public LocusContext getLocus() {
-        return this.locus;
-    }
-
-    /**
-     * gets the region that our read spans
-     *
-     * @return a genome loc that details the region that our read spans.
-     */
-    public GenomeLoc getSequenceLocation() {
-        return GenomeLoc.genomicLocationOf(sam);
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/BasicDataShard.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/BasicDataShard.java
deleted file mode 100644
index 8a7096da1..000000000
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/BasicDataShard.java
+++ /dev/null
@@ -1,36 +0,0 @@
-package org.broadinstitute.sting.gatk.dataSources.shards;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * Created by IntelliJ IDEA.
- * User: aaronmckenna
- * Date: Mar 29, 2009
- * Time: 8:35:16 PM
- * To change this template use File | Settings | File Templates.
- */
-public class BasicDataShard<T> implements DataShard {
-
-    List<T> list = new ArrayList<T>();
-    int index = 0;
-
-    public BasicDataShard(List<T> list) {
-        this.list = list;
-    }
-
-    public boolean hasNext() {
-        if (list.size() > index) {
-            return true;
-        }
-        return false;
-    }
-
-    public T next() {
-        return list.get(index);
-    }
-
-    public void remove() {
-        list.remove(index);
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/DataShard.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/DataShard.java
deleted file mode 100644
index 994fbcb16..000000000
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/DataShard.java
+++ /dev/null
@@ -1,19 +0,0 @@
-package org.broadinstitute.sting.gatk.dataSources.shards;
-
-import java.util.Iterator;
-
-/**
- * User: aaron
- * Date: Mar 26, 2009
- * Time: 2:43:04 PM
- * <p/>
- * 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.
- * <p/>
- * 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.
- */
-public interface DataShard extends Iterator {
-}
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LociShard.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LociShard.java
deleted file mode 100644
index c1f4a5a7f..000000000
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/LociShard.java
+++ /dev/null
@@ -1,99 +0,0 @@
-package org.broadinstitute.sting.gatk.dataSources.shards;
-
-import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.dataSources.datum.LocusDatum;
-import org.broadinstitute.sting.gatk.iterators.LocusIterator;
-import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.utils.GenomeLoc;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- *
- * User: aaron
- * Date: Mar 30, 2009
- * Time: 7:01:56 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 Mar 30, 2009
- * <p/>
- * Class LociShard
- * <p/>
- * This is the loci shard, which are collectively made when a shatter call is made to
- * a data source.
- */
-public class LociShard implements DataShard {
-
-    // our locusIterator
-    private final LocusIterator locusIterator;
-
-    // our reference locusIterator
-    private final ReferenceIterator refIterator;
-
-    // Iterator over rods
-    private final List<ReferenceOrderedData.RODIterator> rodIters;
-
-    // the max number of iterations
-    private final int maxCount;
-
-    // how many iterations we've had
-    private int iterCount = 0;
-
-    public LociShard(LocusIterator locusIterator, ReferenceIterator refIterator, List<ReferenceOrderedData.RODIterator> rodIters, int maxCount) {
-        this.locusIterator = locusIterator;
-        this.maxCount = maxCount;
-        this.refIterator = refIterator;
-        this.rodIters = rodIters;
-    }
-
-    public boolean hasNext() {
-        return locusIterator.hasNext() && maxCount > iterCount;
-    }
-
-    public LocusDatum next() {
-        LocusContext locus = locusIterator.next();
-        ReferenceIterator refSite = refIterator.seekForward(locus.getLocation());
-        locus.setReferenceContig(refSite.getCurrentContig());
-        // Iterate forward to get all reference ordered data covering this locus
-        final List<ReferenceOrderedDatum> rodData = getReferenceOrderedDataAtLocus(rodIters, locus.getLocation());
-        return new LocusDatum(rodData, refSite.getBaseAsChar(), locus);
-    }
-
-    public void remove() {
-        locusIterator.remove();
-    }
-
-    /**
-     * Builds a list of the reference ordered datum at loc from each of the iterators.  This function
-     * assumes you are accessing the data in order.  You can't use this function for random access.  Each
-     * successive call moves you along the file, consuming all data before loc.
-     *
-     * @param rodIters Iterators to access the RODs
-     * @param loc      The location to get the rods at
-     * @return A list of ReferenceOrderDatum at loc.  ROD without a datum at loc will be null in the list
-     */
-    protected List<ReferenceOrderedDatum> getReferenceOrderedDataAtLocus(List<ReferenceOrderedData.RODIterator> rodIters,
-                                                                         final GenomeLoc loc) {
-        List<ReferenceOrderedDatum> data = new ArrayList<ReferenceOrderedDatum>();
-        for (ReferenceOrderedData.RODIterator iter : rodIters) {
-            data.add(iter.seekForward(loc));
-        }
-        return data;
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShard.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShard.java
deleted file mode 100644
index 4ea2349c0..000000000
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShard.java
+++ /dev/null
@@ -1,85 +0,0 @@
-package org.broadinstitute.sting.gatk.dataSources.shards;
-
-import edu.mit.broad.picard.sam.MergingSamRecordIterator;
-import org.broadinstitute.sting.gatk.dataSources.datum.ReadDatum;
-import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
-import net.sf.samtools.SAMRecord;
-
-import java.util.List;
-import java.util.Arrays;
-
-/**
- *
- * User: aaron
- * Date: Mar 30, 2009
- * Time: 5:45:51 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 Mar 30, 2009
- * <p/>
- * Class ReadShard
- * <p/>
- * A read data shard.
- */
-public class ReadShard implements DataShard {
-
-    private MergingSamRecordIterator iterator;
-
-    /**
-     * create the data chunk with an iterator, and a limiter
-     *
-     * @param samIterator
-     */
-    public ReadShard(MergingSamRecordIterator samIterator) {
-        this.iterator = samIterator;
-    }
-
-    /**
-     * do we have a next data point
-     *
-     * @return true if we have a data point
-     */
-    public boolean hasNext() {
-        return iterator.hasNext();
-    }
-
-    public ReadDatum next() {
-        // get the read
-        final SAMRecord read = iterator.next();
-
-        // put the read into a list
-        final List<SAMRecord> reads = Arrays.asList(read);
-
-        // put together the genome location
-        final GenomeLoc loc = GenomeLoc.genomicLocationOf(read);
-
-        // Offset of a single read is always 0
-        List<Integer> offsets = Arrays.asList(0);
-
-        // create the locus
-        final LocusContext locus = new LocusContext(loc, reads, offsets);
-
-        // return the read datum
-        return new ReadDatum(read, locus);
-    }
-
-    /** remove the current pointed to data source */
-    public void remove() {
-        iterator.remove();
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/SAMDataShard.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/SAMDataShard.java
deleted file mode 100644
index b178bdfd9..000000000
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/SAMDataShard.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package org.broadinstitute.sting.gatk.dataSources.shards;
-
-import edu.mit.broad.picard.sam.MergingSamRecordIterator;
-import net.sf.samtools.SAMRecord;
-
-/**
- * Created by IntelliJ IDEA.
- * User: aaronmckenna
- * Date: Mar 29, 2009
- * Time: 8:47:50 PM
- * To change this template use File | Settings | File Templates.
- */
-public class SAMDataShard implements DataShard {
-
-    // our iterator
-    final private MergingSamRecordIterator iterator;
-
-    // divide by reads or by loci
-    private boolean byReads = true;
-
-    // iterator bounds limiter
-    private int lengthCount = 0;
-    private final int limiter;
-
-    public SAMDataShard(MergingSamRecordIterator iterator, int limiter) {
-        this.iterator = iterator;
-        this.limiter = limiter;
-    }
-
-    public SAMDataShard(MergingSamRecordIterator iterator) {
-        this.iterator = iterator;
-        limiter = Integer.MAX_VALUE;
-    }
-
-
-    public boolean hasNext() {
-        return iterator.hasNext() && lengthCount > limiter;
-    }
-
-    public SAMRecord next() {
-        ++lengthCount;
-        return iterator.next();
-    }
-
-    public void remove() {
-        iterator.remove();
-    }
-}