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Oops. Arguments didn't load into applications with non-plugins (basically everything except the GATK). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@617 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2009-05-07 13:37:19 +00:00
parent 4177560543
commit 2f3ab53888
1 changed files with 1 additions and 0 deletions
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java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
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@ -151,6 +151,7 @@ public abstract class CommandLineProgram {
else { else {
parser.parse(args); parser.parse(args);
parser.validate(); parser.validate();
parser.loadArgumentsIntoObject( clp );
} }
// if we're in debug mode, set the mode up // if we're in debug mode, set the mode up