Invalid arguments are not always flagged when stopAtNonOption is false. Make sure stopAnNonOption is true when we do final argument validation.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@245 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 15:58:57 +00:00 · 2009-04-01 15:58:57 +00:00 · 16c2ea4673
parent 7ee792df04
commit 16c2ea4673
1 changed files with 1 additions and 1 deletions
--- 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 ||