diff --git a/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index 39a7e1bd6..d5efd6a72 100755
--- a/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -133,9 +133,9 @@ public class CommandLineGATK extends CommandLineProgram {
     @Override
     protected ArgumentFactory getCustomArgumentFactory() {
         return new ArgumentFactory() {
-            public Object createArgument( Class type, String repr ) {
-                if (type == SAMFileReader.class) {
-                    SAMFileReader samFileReader = new SAMFileReader(new File(repr),true);
+            public Object createArgument( Class type, List<String> repr ) {
+                if (type == SAMFileReader.class && repr.size() == 1) {
+                    SAMFileReader samFileReader = new SAMFileReader(new File(repr.get(0)),true);
                     samFileReader.setValidationStringency(argCollection.strictnessLevel);
                     return samFileReader;
                 }
diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 8422659d6..5648a21b4 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -136,7 +136,8 @@ public class GenomeAnalysisEngine {
         logger.info("Strictness is " + argCollection.strictnessLevel);
 
         // perform validation steps that are common to all the engines
-        genericEngineSetup();
+        engine.setMaximumIterations(argCollection.maximumEngineIterations);
+        engine.initialize();
 
         GenomeLocSortedSet locs = null;
         if (argCollection.intervals != null) {
@@ -192,13 +193,6 @@ public class GenomeAnalysisEngine {
         return microScheduler;
     }
 
-
-    /** commands that get executed for each engine, regardless of the type */
-    private void genericEngineSetup() {
-        engine.setMaximumIterations(argCollection.maximumEngineIterations);
-        engine.initialize();
-    }
-
     /**
      * setup the interval regions, from either the interval file of the genome region string
      *
diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentFactory.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentFactory.java
index 44c9901b4..1b81eacc2 100755
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentFactory.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentFactory.java
@@ -24,6 +24,8 @@
 
 package org.broadinstitute.sting.utils.cmdLine;
 
+import java.util.List;
+
 /**
  * Provides a service whereby the application can provide a mechanism
  * for creating specialty arguments.
@@ -36,5 +38,5 @@ public abstract class ArgumentFactory {
      * @param repr A String representation of the argument.
      * @return
      */
-    public abstract Object createArgument(Class type, String repr);
+    public abstract Object createArgument(Class type, List<String> repr);
 }
diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
index 90e2773ef..6b6cecd4e 100755
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
@@ -270,6 +270,14 @@ public class ParsingEngine {
             return;
 
         if( definition.source.clazz.isAssignableFrom(object.getClass()) ) {
+            if( customArgumentFactory != null ) {
+                Object instance = customArgumentFactory.createArgument(definition.source.field.getType(), match.values());
+                if( instance != null ) {
+                    definition.source.setValue( object, instance );
+                    return;
+                }
+            }
+
             if( !definition.source.isFlag() ) {
                 String[] tokens = match.values().toArray(new String[0]);
                 FieldParser fieldParser = FieldParser.create(definition.source.field);