diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
index bb158111e..0cef2b4f7 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
@@ -276,7 +276,7 @@ public class ArgumentParser {
         Collection<Option> opts = m_options.getOptions();
 
         try {
-            parser.parse(m_options, args, false);
+            parser.parse(m_options, args, !allowIncomplete);
         }
         catch( ParseException e ) {
             boolean isIncomplete = e instanceof MissingArgumentException ||