diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/utils/cmdLine/GATKArgumentCollection.java
deleted file mode 100755
index 7ebf22681..000000000
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/GATKArgumentCollection.java
+++ /dev/null
@@ -1,272 +0,0 @@
-package org.broadinstitute.sting.utils.cmdLine;
-
-import org.broadinstitute.sting.utils.StingException;
-import org.simpleframework.xml.*;
-import org.simpleframework.xml.core.Persister;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.HashMap;
-
-/**
- *
- * User: aaron
- * Date: May 7, 2009
- * Time: 11:46:21 AM
- *
- * 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 May 7, 2009
- * <p/>
- * Class ArgumentObject
- * <p/>
- * Encapsolute the massively large list of possible parameters we take in the Genome Analysis tool
- */
-@Root
-public class GATKArgumentCollection {
-
-    /* our version number */
-    private float versionNumber = 1;
-    private String description = "GATK Arguments";
-
-    /** the constructor */
-    public GATKArgumentCollection() {
-    }
-
-    // parameters and their defaults
-    @ElementList
-    @Argument(fullName = "input_file", shortName = "I", doc = "SAM or BAM file(s)", required = false)
-    public List<File> samFiles = new ArrayList<File>();
-
-    @Element
-    @Argument(fullName = "maximum_reads", shortName = "M", doc = "Maximum number of reads to process before exiting", required = false)
-    public String maximumReads = "-1";
-
-    @Element
-    @Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation (LENIENT|SILENT|STRICT)", required = false)
-    public String strictnessLevel = "strict";
-
-    @Element
-    @Argument(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false)
-    public File referenceFile = null;
-
-    @Element
-    @Argument(fullName = "genome_region", shortName = "L", doc = "Genome region to operation on: from chr:start-end", required = false)
-    public String genomeRegion = null;
-
-    @Element
-    @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
-    public String analysisName = null;
-
-    // parameters and their defaults
-    @ElementMap(entry = "analysis_argument", key = "key", attribute = true, inline = true)
-    public Map<String, String> walkerArgs = new HashMap<String, String>();
-
-    @Element
-    @Argument(fullName = "DBSNP", shortName = "D", doc = "DBSNP file", required = false)
-    public String DBSNPFile = null;
-
-    @Element
-    @Argument(fullName = "hapmap", shortName = "H", doc = "Hapmap file", required = false)
-    public String HAPMAPFile = null;
-
-    @Element
-    @Argument(fullName = "hapmap_chip", shortName = "hc", doc = "Hapmap chip file", required = false)
-    public String HAPMAPChipFile = null;
-
-    @Element
-    @Argument(fullName = "threaded_IO", shortName = "P", doc = "If set, enables threaded I/O operations", required = false)
-    public Boolean EnabledThreadedIO = false;
-
-    @Element
-    @Argument(fullName = "unsafe", shortName = "U", doc = "If set, enables unsafe operations, nothing will be checked at runtime.", required = false)
-    public Boolean unsafe = false;
-
-    @Element
-    @Argument(fullName = "sort_on_the_fly", shortName = "sort", doc = "Maximum number of reads to sort on the fly", required = false)
-    public String maximumReadSorts = null;
-
-    @Element
-    @Argument(fullName = "downsample_to_fraction", shortName = "dfrac", doc = "Fraction [0.0-1.0] of reads to downsample to", required = false)
-    public String downsampleFraction = null;
-
-    @Element
-    @Argument(fullName = "downsample_to_coverage", shortName = "dcov", doc = "Coverage [integer] to downsample to", required = false)
-    public String downsampleCoverage = null;
-
-    @Element
-    @Argument(fullName = "intervals_file", shortName = "V", doc = "File containing list of genomic intervals to operate on. line := <contig> <start> <end>", required = false)
-    public String intervalsFile = null;
-
-    @Element
-    @Argument(fullName = "all_loci", shortName = "A", doc = "Should we process all loci, not just those covered by reads", required = false)
-    public Boolean walkAllLoci = false;
-
-    @Element
-    @Argument(fullName = "disablethreading", shortName = "dt", doc = "Disable experimental threading support.", required = false)
-    public Boolean disableThreading = false;
-
-    /** An output file presented to the walker. */
-    @Element
-    @Argument(fullName = "out", shortName = "o", doc = "An output file presented to the walker.  Will overwrite contents if file exists.", required = false)
-    public String outFileName = null;
-
-    /** An error output file presented to the walker. */
-    @Element
-    @Argument(fullName = "err", shortName = "e", doc = "An error output file presented to the walker.  Will overwrite contents if file exists.", required = false)
-    public String errFileName = null;
-
-    /** A joint file for both 'normal' and error output presented to the walker. */
-    @Element
-    @Argument(fullName = "outerr", shortName = "oe", doc = "A joint file for 'normal' and error output presented to the walker.  Will overwrite contents if file exists.", required = false)
-    public String outErrFileName = null;
-
-    /** How many threads should be allocated to this analysis. */
-    @Element
-    @Argument(fullName = "numthreads", shortName = "nt", doc = "How many threads should be allocated to running this analysis.", required = false)
-    public int numberOfThreads = 1;
-
-    @ElementList
-    @Argument(fullName = "rodBind", shortName = "B", doc = "", required = false)
-    public ArrayList<String> RODBindings = new ArrayList<String>();
-
-    /**
-     * marshal the data out to a object
-     *
-     * @param collection the GATKArgumentCollection to load into
-     * @param outputFile the file to write to
-     */
-    public static void marshal(GATKArgumentCollection collection, String outputFile) {
-        Serializer serializer = new Persister();
-        File result = new File(outputFile);
-        try {
-            serializer.write(collection, result);
-        } catch (Exception e) {
-            throw new StingException("Failed to marshal the data from the file " + outputFile, e);
-        }
-    }
-
-    /**
-     * unmashall the object from a configuration file
-     *
-     * @param filename the filename to marshal from
-     */
-    public static GATKArgumentCollection unmarshal(String filename) {
-        Serializer serializer = new Persister();
-        File source = new File(filename);
-        try {
-            GATKArgumentCollection example = serializer.read(GATKArgumentCollection.class, source);
-            return example;
-        } catch (Exception e) {
-            throw new StingException("Failed to marshal the data to file " + filename, e);
-        }
-    }
-
-    /**
-     * test equality between two arg collections.  This functions defines the statement:
-     * "not fun to write"
-     * @param other the other collection
-     * @return true if they're equal
-     */
-    public boolean equals(GATKArgumentCollection other) {        
-        if (other.samFiles.size() != samFiles.size()) {
-            return false;
-        }
-        for (int x = 0; x < samFiles.size(); x++) {
-            if (!samFiles.get(x).equals(other.samFiles.get(x))) {
-                return false;
-            }
-        }
-        if (other.walkerArgs.size() != walkerArgs.size()) {
-            return false;
-        }
-        for (String s : walkerArgs.keySet()) {
-            if (!other.walkerArgs.containsKey(s)) {
-                return false;
-            }
-        }
-        if (other.RODBindings.size() != RODBindings.size()) {
-            return false;
-        }
-        for (int x = 0; x < RODBindings.size(); x++) {
-            if (!RODBindings.get(x).equals(other.RODBindings.get(x))) {
-                return false;
-            }
-        }
-        if (!other.samFiles.equals(this.samFiles)) {
-            return false;
-        }
-        if (!other.maximumReads.equals(this.maximumReads)) {
-            return false;
-        }
-        if (!other.strictnessLevel.equals(this.strictnessLevel)) {
-            return false;
-        }
-        if (!other.referenceFile.equals(this.referenceFile)) {
-            return false;
-        }
-        if (!other.genomeRegion.equals(this.genomeRegion)) {
-            return false;
-        }
-        if (!other.analysisName.equals(this.analysisName)) {
-            return false;
-        }
-        if (!other.DBSNPFile.equals(this.DBSNPFile)) {
-            return false;
-        }
-        if (!other.HAPMAPFile.equals(this.HAPMAPFile)) {
-            return false;
-        }
-        if (!other.HAPMAPChipFile.equals(this.HAPMAPChipFile)) {
-            return false;
-        }
-        if (!other.EnabledThreadedIO.equals(this.EnabledThreadedIO)) {
-            return false;
-        }
-        if (!other.unsafe.equals(this.unsafe)) {
-            return false;
-        }
-        if (!other.maximumReadSorts.equals(this.maximumReadSorts)) {
-            return false;
-        }
-        if (!other.downsampleFraction.equals(this.downsampleFraction)) {
-            return false;
-        }
-        if (!other.downsampleCoverage.equals(this.downsampleCoverage)) {
-            return false;
-        }
-        if (!other.intervalsFile.equals(this.intervalsFile)) {
-            return false;
-        }
-        if (!other.walkAllLoci.equals(this.walkAllLoci)) {
-            return false;
-        }
-        if (!other.outFileName.equals(this.outFileName)) {
-            return false;
-        }
-        if (!other.errFileName.equals(this.errFileName)) {
-            return false;
-        }
-        if (!other.outErrFileName.equals(this.outErrFileName)) {
-            return false;
-        }
-        if (other.numberOfThreads != this.numberOfThreads) {
-            return false;
-        }
-        return true;
-    }
-}
diff --git a/java/test/org/broadinstitute/sting/utils/cmdLine/GATKArgumentCollectionTest.java b/java/test/org/broadinstitute/sting/utils/cmdLine/GATKArgumentCollectionTest.java
deleted file mode 100755
index f52351260..000000000
--- a/java/test/org/broadinstitute/sting/utils/cmdLine/GATKArgumentCollectionTest.java
+++ /dev/null
@@ -1,125 +0,0 @@
-package org.broadinstitute.sting.utils.cmdLine;
-
-import org.broadinstitute.sting.BaseTest;
-import org.junit.After;
-import static org.junit.Assert.fail;
-import org.junit.Before;
-import org.junit.Test;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-/**
- *
- * User: aaron
- * Date: May 7, 2009
- * Time: 1:12:58 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 May 7, 2009
- * <p/>
- * Class GATKArgumentCollection
- * <p/>
- * A descriptions should go here. Blame aaron if it's missing.
- */
-public class GATKArgumentCollectionTest extends BaseTest {
-
-    // our collection of arguments
-    private GATKArgumentCollection collect;
-
-    // where to write our xml file
-    private String xmlFileLoc = "testfile.xml";
-
-    /** setup our test */
-    @Before
-    public void setup() {
-        collect = new GATKArgumentCollection();
-    }
-
-    /** destroy the temp file */
-    @After
-    public void takedown() {
-        File f = new File(xmlFileLoc);
-        if (f.exists()) {
-            f.delete();
-        }
-    }
-
-    private void setupCollection() {
-        // parameters and their defaults
-        Map<String, String> wArgs = new HashMap<String, String>();
-        wArgs.put("wArgType1", "Arg1");
-        wArgs.put("wArgType2", "Arg2");
-        wArgs.put("wArgType3", "Arg3");
-        collect.walkerArgs = wArgs;
-
-        List<File> input = new ArrayList<File>();
-        input.add(new File("test.file"));
-        collect.samFiles = input;
-        collect.maximumReads = "-1";
-        collect.strictnessLevel = "strict";
-        collect.referenceFile = new File("referenceFile".toLowerCase());
-        collect.genomeRegion = "genomeRegion".toLowerCase();
-        collect.analysisName = "analysisName".toLowerCase();
-        collect.DBSNPFile = "DBSNPFile".toLowerCase();
-        collect.HAPMAPFile = "HAPMAPFile".toLowerCase();
-        collect.HAPMAPChipFile = "HAPMAPChipFile".toLowerCase();
-        collect.EnabledThreadedIO = true;
-        collect.unsafe = false;
-        collect.maximumReadSorts = "maximumReadSorts".toLowerCase();
-        collect.downsampleFraction = "downsampleFraction".toLowerCase();
-        collect.downsampleCoverage = "downsampleCoverage".toLowerCase();
-        collect.intervalsFile = "intervalsFile".toLowerCase();
-        collect.walkAllLoci = true;
-        collect.disableThreading = false;
-        collect.outFileName = "outFileName".toLowerCase();
-        collect.errFileName = "errFileName".toLowerCase();
-        collect.outErrFileName = "outErrFileName".toLowerCase();
-        collect.numberOfThreads = 1;
-
-        // make some rod bindings up
-        ArrayList<String> fakeBindings = new ArrayList<String>();
-        fakeBindings.add("Bind1");
-        fakeBindings.add("Bind2");
-        fakeBindings.add("Bind3");
-
-        collect.RODBindings = fakeBindings;
-    }
-
-
-    /** test the output of an XML file in the arg collection */
-    @Test
-    public void testOutput() {
-        setupCollection();
-
-        GATKArgumentCollection.marshal(collect, xmlFileLoc);
-        GATKArgumentCollection collection = GATKArgumentCollection.unmarshal(xmlFileLoc);
-        if (!collect.equals(collection)) {
-            fail("Collections not equal");
-        }
-    }
-
-
-    /** test the output of an XML file in the arg collection */
-    @Test
-    public void testInput() {
-        setupCollection();
-        GATKArgumentCollection.marshal(collect, xmlFileLoc);
-    }
-}