diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
index 0cef2b4f7..8b144c49b 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
@@ -269,11 +269,10 @@ public class ArgumentParser {
      * exit the program
      *
      * @param args the command line arguments we recieved
-     * @param args whether to allow incomplete command-line arguments
+     * @param allowIncomplete whether to allow incomplete command-line arguments
      */
     public void processArgs(String[] args, boolean allowIncomplete) throws ParseException {
         OurPosixParser parser = new OurPosixParser();
-        Collection<Option> opts = m_options.getOptions();
 
         try {
             parser.parse(m_options, args, !allowIncomplete);
@@ -292,7 +291,6 @@ public class ArgumentParser {
         // Apache CLI can ignore unrecognized arguments with a boolean flag, but
         // 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.
         this.cmd = parser.getCmd();
     }
 
diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java b/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
index b8ed4f60e..b72c8ba4b 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
@@ -142,6 +142,10 @@ public abstract class CommandLineProgram {
                 for( Class argumentSource: argumentSources )
                     clp.addArgumentSource( argumentSource );
                 clp.m_parser.processArgs(args, false);
+
+                // HACK: Load arguments into object again.  Apache CLI always stops processing when an option
+                //       is unrecognized, so if core arguments were intermixed with walker arguments, stop processing.
+                clp.m_parser.loadArgumentsIntoObject( clp );
             }
             else {
                 clp.m_parser.processArgs(args, false);