diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
index c90cd2c2b..bfa6c3e72 100644
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -24,7 +24,7 @@ import java.util.HashMap;
 import java.util.List;
 
 public class GenomeAnalysisTK extends CommandLineProgram {
-
+    public static GenomeAnalysisTK Instance = null;
 
     // parameters and their defaults
     public File INPUT_FILE;
@@ -43,7 +43,6 @@ public class GenomeAnalysisTK extends CommandLineProgram {
 
     // our walker manager
     private WalkerManager walkerManager = null;
-    private Walker my_walker = null;
 
     public String pluginPathName = null;
     private TraversalEngine engine = null;
@@ -88,7 +87,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
      * @return List of walkers to load dynamically.
      */
     @Override
-    protected Object[] getArgumentSources() {
+    protected Class[] getArgumentSources() {
         if( Analysis_Name == null )
             throw new IllegalArgumentException("Must provide analysis name");
 
@@ -97,16 +96,20 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         if( !walkerManager.doesWalkerExist(Analysis_Name) )
             throw new IllegalArgumentException("Invalid analysis name");
 
-        my_walker = walkerManager.getWalkerByName(Analysis_Name);
+        return new Class[] { walkerManager.getWalkerClassByName(Analysis_Name) };
+    }
 
-        return new Object[] { my_walker };
+    @Override
+    protected String getArgumentSourceName( Class argumentSource ) {
+        return WalkerManager.getWalkerName( (Class<Walker>)argumentSource );    
     }
 
     /**
      * Required main method implementation.
      */
     public static void main(String[] argv) {
-        start(new GenomeAnalysisTK(), argv);
+        Instance = new GenomeAnalysisTK();
+        start(Instance, argv);
     }
 
     protected int execute() {
@@ -175,12 +178,17 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         engine.setSortOnFly(ENABLED_SORT_ON_FLY);
         engine.setThreadedIO(ENABLED_THREADED_IO);
         engine.initialize();
-        //engine.testReference();
 
-        //LocusWalker<Integer,Integer> walker = new PileupWalker();
-
-        if( my_walker == null )
-            throw new RuntimeException( "Sanity check failed -- no walker present." );
+        Walker my_walker = null;
+        try {
+            my_walker = walkerManager.createWalkerByName( Analysis_Name );
+        }
+        catch( InstantiationException ex ) {
+            throw new RuntimeException( "Unable to instantiate walker.", ex );
+        }
+        catch( IllegalAccessException ex ) {
+            throw new RuntimeException( "Unable to access walker", ex );
+        }
 
         // Try to get the walker specified
         try {
diff --git a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
index 0feb0854e..03658a1da 100755
--- a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
@@ -21,6 +21,7 @@ import java.util.jar.JarEntry;
 import java.util.jar.JarInputStream;
 
 import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 /**
@@ -31,16 +32,16 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
  * To change this template use File | Settings | File Templates.
  */
 public class WalkerManager {
-    
-    private Map<String,Walker> walkers = null;
 
+    private Map<String,Class> walkers;
+    
     public WalkerManager( String pluginDirectory ) {
         try {
-            List<Class> walkerClasses = new ArrayList<Class>();
+            List<Class> walkerCandidates = new ArrayList<Class>();
 
             // Load all classes that live in this jar.
             final File location = getThisLocation();
-            walkerClasses.addAll( loadClassesFromLocation( location ) );
+            walkerCandidates.addAll( loadClassesFromLocation( location ) );
 
             // Load all classes that live in the extension path.
             if(pluginDirectory == null)
@@ -50,29 +51,21 @@ public class WalkerManager {
             File extensionPath = new File( pluginDirectory );
             if(extensionPath.exists()) {
                 List<String> filesInPath = findFilesInPath( extensionPath, "", "class", false );
-                walkerClasses.addAll( loadExternalClasses( extensionPath, filesInPath ) );
+                walkerCandidates.addAll( loadExternalClasses( extensionPath, filesInPath ) );
             }
 
-            walkerClasses = filterWalkers(walkerClasses);
+            walkerCandidates = filterWalkers(walkerCandidates);
 
-            if(walkerClasses.isEmpty())
+            if(walkerCandidates.isEmpty())
                 throw new RuntimeException("No walkers were found.");            
 
-            walkers = instantiateWalkers( walkerClasses );
+            walkers = createWalkerDatabase( walkerCandidates );
         }
         // IOExceptions here are suspect; they indicate that the WalkerManager can't open its containing jar.
         // Wrap in a RuntimeException.
         catch(IOException ex) {
             throw new RuntimeException(ex);
         }
-        // The following two catches are more 'expected'; someone might add a walker that can't be instantiated.
-        // TODO: Should these exceptions be handled differently?  Handling them like IOExceptions for the moment.
-        catch(InstantiationException ex) {
-            throw new RuntimeException(ex);
-        }
-        catch(IllegalAccessException ex) {
-            throw new RuntimeException(ex);
-        }
     }
 
     /**
@@ -89,9 +82,14 @@ public class WalkerManager {
      * @param walkerName Name of the walker to retrieve.
      * @return The walker object if found; null otherwise.
      */
-    public Walker getWalkerByName(String walkerName) {
-        Walker walker = walkers.get(walkerName);
-        return walker;
+    public Walker createWalkerByName(String walkerName)
+            throws InstantiationException, IllegalAccessException {
+        Class walker = walkers.get(walkerName);
+        return (Walker)walker.newInstance();
+    }
+
+    public Class getWalkerClassByName( String walkerName ) {
+        return walkers.get(walkerName);
     }
 
     /**
@@ -224,7 +222,7 @@ public class WalkerManager {
      * TODO: Test recursive traversal in the presence of a symlink.
      */
     private List<String> findFilesInPath(final File basePath, final String relativePrefix, final String extension, boolean recursive) {
-        List<String> filesInPath = new ArrayList();
+        List<String> filesInPath = new ArrayList<String>();
 
         File[] contents = basePath.listFiles( new OrFilenameFilter( new DirectoryFilter(), new ExtensionFilter( extension ) ) );
         for( File content: contents ) {
@@ -302,21 +300,37 @@ public class WalkerManager {
     /**
      * Instantiate the list of walker classes.  Add them to the walker hashmap.
      * @param walkerClasses Classes to instantiate.
-     * @throws InstantiationException
-     * @throws IllegalAccessException
+     * @return map of walker name to walker.
      */
-    private Map<String,Walker> instantiateWalkers(List<Class> walkerClasses)
-            throws InstantiationException, IllegalAccessException {
-        Map<String,Walker> walkers = new HashMap<String,Walker>();
-
-        for(Class walkerClass : walkerClasses) {
-            Walker walker = (Walker)walkerClass.newInstance();
-            String walkerName = walker.getName();
+    private Map<String,Class> createWalkerDatabase(List<Class> walkerClasses) {
+        Map<String,Class> walkers = new HashMap<String,Class>();
 
+        for(Class<Walker> walkerClass : walkerClasses) {
+            String walkerName = getWalkerName( walkerClass );
             System.out.printf("* Adding module %s%n", walkerName);            
-            walkers.put(walkerName,walker);
+            walkers.put(walkerName,walkerClass);
         }
 
         return walkers;
     }
+
+    /**
+     * Create a name for this type of walker.
+     * @param walkerType The type of walker.
+     * @return A name for this type of walker.
+     */
+    public static String getWalkerName( Class<Walker> walkerType ) {
+        String walkerName = "";
+
+        if( walkerType.getAnnotation( WalkerName.class ) != null )
+            walkerName = walkerType.getAnnotation( WalkerName.class ).value().trim();
+
+        if( walkerName.length() == 0 ) {
+            walkerName = walkerType.getSimpleName();
+            if( walkerName.endsWith("Walker") )
+                walkerName = walkerName.substring( 0,walkerName.lastIndexOf("Walker") );
+        }
+
+        return walkerName;
+    }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
index 2f46fbcc8..dc69ab344 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers;
 
+import org.broadinstitute.sting.gatk.GenomeAnalysisTK;
+
 /**
  * Created by IntelliJ IDEA.
  * User: hanna
@@ -9,13 +11,19 @@ package org.broadinstitute.sting.gatk.walkers;
  */
 public abstract class Walker {
     // TODO: Can a walker be templatized so that map and reduce live here?
-    public String getName() {
-        // Return name of class, trimming 'Walker' from the end if present.
-        String className = getClass().getSimpleName();
-        if(className.endsWith(Walker.class.getSimpleName()))
-            return className.substring(0,className.lastIndexOf(Walker.class.getSimpleName()));
-        else
-            return className;
+
+    protected Walker() {
+        GenomeAnalysisTK.Instance.loadArgumentsIntoObject(this);
+    }
+
+    /**
+     * Retrieve the toolkit, for peering into internal structures that can't
+     * otherwise be read.  Use sparingly, and discuss uses with software engineering
+     * team.
+     * @return The genome analysis toolkit.
+     */
+    protected GenomeAnalysisTK getToolkit() {
+        return GenomeAnalysisTK.Instance;
     }
 
     public void initialize() { }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java b/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java
new file mode 100755
index 000000000..0e4d40675
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java
@@ -0,0 +1,21 @@
+package org.broadinstitute.sting.gatk.walkers;
+
+import java.lang.annotation.Documented;
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: hanna
+ * Date: Mar 26, 2009
+ * Time: 3:00:16 PM
+ * To change this template use File | Settings | File Templates.
+ */
+@Documented
+@Retention(RetentionPolicy.RUNTIME)
+@Target(ElementType.TYPE)
+public @interface WalkerName {
+    public String value() default "";
+}
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java
index 2788ec176..70f08e075 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java
@@ -2,6 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.gatk.LocusContext;
 
 /**
@@ -11,13 +12,10 @@ import org.broadinstitute.sting.gatk.LocusContext;
  * Time: 3:22:14 PM
  * To change this template use File | Settings | File Templates.
  */
+@WalkerName("Aligned_Reads_Histogram")
 public class AlignedReadsHistoWalker extends ReadWalker<Integer, Integer> {
     long[] alignCounts = new long[51];
 
-    public String getName() {
-        return "Aligned_Reads_Histogram";
-    }
-
     public void initialize() {
         for ( int i = 0; i < alignCounts.length; i++ ) {
             alignCounts[i] = 0;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java
index 45e87f560..282688efb 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.Utils;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 
@@ -10,15 +11,12 @@ import java.util.Iterator;
 import java.util.List;
 import static java.lang.reflect.Array.*;
 
+@WalkerName("Base_Quality_Dump")
 public class BaseQualityDumpWalker extends ReadWalker<Integer, Integer> {
 
     protected final int MIN_TARGET_EDIT_DISTANCE = 0; //5;
     protected final int MAX_TARGET_EDIT_DISTANCE = 4; //10;
 
-    public String getName() {
-        return "Base_Quality_Dump";
-    }
-
     // Do we actually want to operate on the context?
     public boolean filter(LocusContext context, SAMRecord read) {
 	    // we only want aligned reads
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java
index 07c0b5be1..0decc9ae9 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java
@@ -2,6 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.gatk.LocusContext;
 
 /**
@@ -11,13 +12,10 @@ import org.broadinstitute.sting.gatk.LocusContext;
  * Time: 3:22:14 PM
  * To change this template use File | Settings | File Templates.
  */
+@WalkerName("Base_Quality_Histogram")
 public class BaseQualityHistoWalker extends ReadWalker<Integer, Integer> {
     long[] qualCounts = new long[100];
 
-    public String getName() {
-        return "Base_Quality_Histogram";
-    }
-
     public void initialize() {
         for ( int i = 0; i < this.qualCounts.length; i++ ) {
             this.qualCounts[i] = 0;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java
index 974691a1a..b42834c49 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.Utils;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 
@@ -10,11 +11,8 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
+@WalkerName("CountMismatches")
 public class MismatchCounterWalker extends ReadWalker<Integer, Integer> {
-    public String getName() {
-        return "CountMismatches";
-    }
-
     public Integer map(LocusContext context, SAMRecord read) {
         int nMismatches = 0;
         
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
index 4ce245923..10ef4a4e5 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.Utils;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 
@@ -10,16 +11,13 @@ import java.util.Iterator;
 import java.util.List;
 import static java.lang.reflect.Array.*;
 
+@WalkerName("Mismatch_Histogram")
 public class MismatchHistoWalker extends ReadWalker<Integer, Integer> {
 
     protected long[] mismatchCounts = new long[0];
     protected final int MIN_TARGET_EDIT_DISTANCE = 5;
     protected final int MAX_TARGET_EDIT_DISTANCE = 10;
 
-    public String getName() {
-        return "Mismatch_Histogram";
-    }
-
     // Do we actually want to operate on the context?
     public boolean filter(LocusContext context, SAMRecord read) {
 	    // we only want aligned reads
diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
index 7c95e4fed..e4709fc6e 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
@@ -9,7 +9,7 @@ import java.lang.reflect.Field;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Modifier;
 import java.lang.reflect.ParameterizedType;
-import java.lang.reflect.Type;
+import java.util.Arrays;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -37,8 +37,11 @@ public class ArgumentParser {
     // what program are we parsing for
     private String programName;
 
+    // the command-line options received.
+    private CommandLine cmd;
+
     // where we eventually want the values to land
-    private HashMap<String, Pair<Object,Field>> m_storageLocations = new HashMap<String, Pair<Object,Field>>();
+    private HashMap<String,Field> m_storageLocations = new HashMap<String,Field>();
 
     // create Options object
     protected Options m_options = new Options();
@@ -112,7 +115,7 @@ public class ArgumentParser {
      * @param opt        the option
      * @param field      what field it should be stuck into on the calling class
      */
-    private void AddToOptionStorage(Option opt, Pair<Object,Field> field ) {
+    private void AddToOptionStorage(Option opt, Field field ) {
         // first check to see if we've already added an option with the same name
         if (m_options.hasOption( opt.getOpt() ))
             throw new IllegalArgumentException(opt.getOpt() + " was already added as an option");
@@ -132,10 +135,10 @@ public class ArgumentParser {
      * Used locally to add a group of mutually exclusive options to options storage.
      * @param options A list of pairs of param, field to add.
      */
-    private void AddToOptionStorage( List<Pair<Option,Pair<Object,Field>>> options ) {
+    private void AddToOptionStorage( List<Pair<Option,Field>> options ) {
         OptionGroup optionGroup = new OptionGroup();
 
-        for( Pair<Option,Pair<Object,Field>> option: options ) {
+        for( Pair<Option,Field> option: options ) {
             if (m_options.hasOption(option.first.getOpt()) )
                 throw new IllegalArgumentException(option.first.getOpt() + " was already added as an option");
 
@@ -147,9 +150,9 @@ public class ArgumentParser {
         m_options.addOptionGroup(optionGroup);
     }
 
-    private Pair<Object,Field> getField( Object obj, String fieldName ) {
+    private Field getField( Object obj, String fieldName ) {
         try {
-            return new Pair<Object,Field>( obj, obj.getClass().getField(fieldName) );
+            return obj.getClass().getField(fieldName);
         } catch (NoSuchFieldException e) {
             logger.fatal("Failed to find the field specified by the fieldname parameter.");
             throw new RuntimeException(e.getMessage());
@@ -283,14 +286,24 @@ public class ArgumentParser {
         // you can't get to the unparsed args.  Override PosixParser with a class
         // that can reach in and extract the protected command line.
         // TODO: Holy crap this is wacky.  Find a cleaner way.
-        CommandLine cmd = parser.getCmd();
+        this.cmd = parser.getCmd();
+    }
+
+    public void loadArgumentsIntoObject( Object obj ) {
+        Collection<Option> opts = m_options.getOptions();
 
         // logger.info("We have " + opts.size() + " options");
         for (Option opt : opts) {
             if (cmd.hasOption(opt.getOpt())) {
                 //logger.info("looking at " + m_storageLocations.get(opt.getLongOpt()));
-                Object obj = m_storageLocations.get(opt.getLongOpt()).first;
-                Field field = m_storageLocations.get(opt.getLongOpt()).second;
+                Field field = m_storageLocations.get(opt.getLongOpt());
+
+                // Check to see if the object contains the specified field.  Iterate through
+                // the array rather than doing a name lookup in case field names overlap between
+                // multiple classes in the application.
+                List<Field> fieldsInObj = Arrays.asList(obj.getClass().getFields());
+                if( !fieldsInObj.contains(field) )
+                    continue;
 
                 try {
                     if (opt.hasArg())
@@ -316,19 +329,19 @@ public class ArgumentParser {
      * Extract arguments stored in annotations from fields of a given class.
      * @param source Source of arguments, probably provided through Argument annotation.
      */
-    public void addArgumentSource( Object source ) {
-        Field[] fields = source.getClass().getFields();
+    public void addArgumentSource( CommandLineProgram clp, Class source ) {
+        Field[] fields = source.getFields();
 
         for( Set<Field> optionGroup: groupExclusiveOptions(fields) ) {
-            List<Pair<Option,Pair<Object,Field>>> options = new ArrayList<Pair<Option,Pair<Object,Field>>>();
+            List<Pair<Option,Field>> options = new ArrayList<Pair<Option,Field>>();
             for( Field field: optionGroup ) {
                 Argument argument = field.getAnnotation(Argument.class);
-                Option option = createOptionFromField( source, field, argument );
-                options.add( new Pair<Option,Pair<Object,Field>>( option, new Pair<Object,Field>( source,field) ) );
+                Option option = createOptionFromField( clp.getArgumentSourceName( source ), field, argument );
+                options.add( new Pair<Option,Field>( option, field ) );
             }
 
             if( options.size() == 1 )
-                AddToOptionStorage( options.get(0).first, new Pair<Object,Field>( source, options.get(0).second.second ) );
+                AddToOptionStorage( options.get(0).first, options.get(0).second );
             else {
                 AddToOptionStorage( options );
             }
@@ -392,7 +405,7 @@ public class ArgumentParser {
      * @param field Field
      * @return Option representing the field options.
      */
-    private Option createOptionFromField( Object source, Field field, Argument argument ) {
+    private Option createOptionFromField( String sourceName, Field field, Argument argument ) {
 
         String fullName = (argument.fullName().length() != 0) ? argument.fullName() : field.getName().trim().toLowerCase();
         String shortName = (argument.shortName().length() != 0) ? argument.shortName() : fullName.substring(0,1);
@@ -404,7 +417,7 @@ public class ArgumentParser {
         if( isFlag && isCollection )
             throw new IllegalArgumentException("Can't have an array of flags.");
 
-        String description = String.format("[%s] %s", source, argument.doc());
+        String description = String.format("[%s] %s", sourceName, argument.doc());
 
         OptionBuilder ob = OptionBuilder.withLongOpt(fullName);
         if( !isFlag ) {
@@ -413,7 +426,7 @@ public class ArgumentParser {
         }
         if( argument.required() ) {
             ob = ob.isRequired();
-            description = String.format("[%s] (Required Option) %s", source, argument.doc());
+            description = String.format("[%s] (Required Option) %s", sourceName, argument.doc());
         }
         if( description.length() != 0 ) ob = ob.withDescription( description );
 
diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java b/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
index 273883bd0..829657975 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
@@ -81,7 +81,14 @@ public abstract class CommandLineProgram {
      * Provide a list of object to inspect, looking for additional command-line arguments.
      * @return A list of objects to inspect.
      */
-    protected Object[] getArgumentSources() { return new Object[] {}; }
+    protected Class[] getArgumentSources() { return new Class[] {}; }
+
+    /**
+     * Name this argument source.  Provides the (full) class name as a default.
+     * @param source The argument source.
+     * @return a name for the argument source.
+     */
+    protected String getArgumentSourceName( Class source ) { return source.toString(); }
 
     /**
      * this is the function that the inheriting class can expect to have called
@@ -128,13 +135,16 @@ public abstract class CommandLineProgram {
             if( clp.canAddArgumentsDynamically() ) {
                 // if the command-line program can toss in extra args, fetch them and reparse the arguments.
                 clp.m_parser.processArgs(args, true);
-                Object[] argumentSources = clp.getArgumentSources();
-                for( Object argumentSource: argumentSources )
+                clp.m_parser.loadArgumentsIntoObject( clp );
+
+                Class[] argumentSources = clp.getArgumentSources();
+                for( Class argumentSource: argumentSources )
                     clp.addArgumentSource( argumentSource );
                 clp.m_parser.processArgs(args, false);
             }
             else {
                 clp.m_parser.processArgs(args, false);
+                clp.m_parser.loadArgumentsIntoObject( clp );
             }
 
             // if we're in debug mode, set the mode up
@@ -201,6 +211,15 @@ public abstract class CommandLineProgram {
         }
     }
 
+    /**
+     * Find fields in the object obj that look like command-line arguments, and put command-line
+     * arguments into them.
+     * @param obj Object to inspect for command line arguments.
+     */
+    public void loadArgumentsIntoObject( Object obj ) {
+        m_parser.loadArgumentsIntoObject( obj );
+    }
+
     /**
      * generateHeaderInformation
      * <p/>
@@ -261,8 +280,8 @@ public abstract class CommandLineProgram {
      * probably a class with @argument annotations.
      * @param source
      */
-    private void addArgumentSource( Object source ) {
-        m_parser.addArgumentSource(source);
+    private void addArgumentSource( Class source ) {
+        m_parser.addArgumentSource( this, source );
     }
 
     /**