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gatk-3.8
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Always create output files, even if no output was written to them. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1627 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-09-15 17:58:14 +00:00
parent 8f9dd03e87
commit b69eb208a6
3 changed files with 21 additions and 6 deletions
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2
java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
View File

@ -142,6 +142,8 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
printOnTraversalDone(result);
getOutputTracker().close();
return result;
}

2
java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
View File

@ -59,6 +59,8 @@ public class LinearMicroScheduler extends MicroScheduler {
printOnTraversalDone(result);
getOutputTracker().close();
return accumulator;
}

23
java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
View File

@ -65,19 +65,16 @@ public abstract class OutputTracker {
// Otherwise, initialize them separately.
if( outFileName != null && outFileName.equals(errFileName) ) {
outStub = errStub = new OutputStreamStub(new File(outFileName));
outStub.register(this);
outputs.put(outStub,null);
addOutput(outStub);
}
else {
outStub = (outFileName != null) ? new OutputStreamStub(new File(outFileName))
: new OutputStreamStub(System.out);
outStub.register(this);
outputs.put(outStub,null);
addOutput(outStub);
errStub = (errFileName != null) ? new OutputStreamStub(new File(errFileName))
: new OutputStreamStub(System.err);
errStub.register(this);
outputs.put(errStub,null);
addOutput(errStub);
}
}
@ -127,6 +124,20 @@ public abstract class OutputTracker {
outputs.put(stub,null);
}
/**
* Close down all existing output streams.
*/
public void close() {
for( Stub stub: outputs.keySet() ) {
// If the stream hasn't yet been created, create it so that there's at least an empty file present.
if( outputs.get(stub) == null )
getTargetStream(stub);
// Close down the storage.
outputs.get(stub).close();
}
}
/**
* Collects the target stream for this data.
* @param stub The stub for this stream.