diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java b/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
index 5a216e72b..495229f3c 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
@@ -151,6 +151,7 @@ public abstract class CommandLineProgram {
             else {
                 parser.parse(args);
                 parser.validate();
+                parser.loadArgumentsIntoObject( clp );
             }
 
             // if we're in debug mode, set the mode up