diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/utils/cmdLine/GATKArgumentCollection.java
new file mode 100755
index 000000000..7ebf22681
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/GATKArgumentCollection.java
@@ -0,0 +1,272 @@
+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
new file mode 100755
index 000000000..f52351260
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/utils/cmdLine/GATKArgumentCollectionTest.java
@@ -0,0 +1,125 @@
+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);
+    }
+}