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gatk-3.8
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Check for the existence of the module name and return error rather than throwing an exception if not found. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@23 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2009-03-04 00:15:35 +00:00
parent a81a1bdbb4
commit e938dbda47
1 changed files with 13 additions and 3 deletions
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16
java/src/edu/mit/broad/sting/atk/AnalysisTK.java
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@ -96,16 +96,26 @@ public class AnalysisTK extends CommandLineProgram {
}
//LocusWalker<Integer,Integer> walker = new PileupWalker();
// Try to get the module specified
Object my_module;
if (MODULES.containsKey(Analysis_Name)) {
my_module = MODULES.get(Analysis_Name);
}else{
System.out.println("Could not find module "+Analysis_Name);
return 0;
}
try {
LocusWalker<?, ?> walker = (LocusWalker<?, ?>)MODULES.get(Analysis_Name);
LocusWalker<?, ?> walker = (LocusWalker<?, ?>)my_module;
engine.traverseByLoci(walker);
}
catch ( java.lang.ClassCastException e ) {
// I guess we're a read walker LOL
ReadWalker<?, ?> walker = (ReadWalker<?, ?>)MODULES.get(Analysis_Name);
ReadWalker<?, ?> walker = (ReadWalker<?, ?>)my_module;
engine.traverseByRead(walker);
}
return 0;
}
}
}