Tweak the arguments passed to the command-line arguments parser so that it fails less often for invalid arguments.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@560 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java

@@ -280,7 +280,7 @@ public class ArgumentParser {
         OurPosixParser parser = new OurPosixParser();
 
         try {
-            parser.parse(m_options, args, !allowIncomplete);
+            parser.parse(m_options, args, false);
         }
         catch( ParseException e ) {
             boolean isIncomplete = e instanceof MissingArgumentException ||