zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Catch and rethrow the walker's required argument, so that command-line arguments will be displayed when the GATK throws an argument exception. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@765 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-20 19:17:16 +00:00
parent dc748d9c9c
commit 3cad580655
1 changed files with 7 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
View File

@ -7,6 +7,7 @@ import org.broadinstitute.sting.utils.xReadLines;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.cmdLine.ArgumentCollection;
import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
import org.broadinstitute.sting.utils.cmdLine.ArgumentException;
import java.io.FileNotFoundException;
import java.io.File;
@ -93,7 +94,12 @@ public class CommandLineGATK extends CommandLineProgram {
this.argCollection.analysisName = this.analysisName;
try {
GATKEngine = new GenomeAnalysisEngine(argCollection, mWalker);
} catch (StingException exp) {
}
catch (ArgumentException ex) {
// Rethrow argument exceptions. Let the command-line argument do what it's designed to do.
throw ex;
}
catch (StingException exp) {
System.err.println("Caught StingException. It's message is " + exp.getMessage());
exp.printStackTrace();
return -1;