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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
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hanna 2009-04-01 15:58:57 +00:00
parent 7ee792df04
commit 16c2ea4673
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
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@ -276,7 +276,7 @@ public class ArgumentParser {
Collection<Option> opts = m_options.getOptions(); Collection<Option> opts = m_options.getOptions();
try { try {
parser.parse(m_options, args, false); parser.parse(m_options, args, !allowIncomplete);
} }
catch( ParseException e ) { catch( ParseException e ) {
boolean isIncomplete = e instanceof MissingArgumentException || boolean isIncomplete = e instanceof MissingArgumentException ||