Package org.broadinstitute.gatk.engine.io.storage

Examples of org.broadinstitute.gatk.engine.io.storage.Storage

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* @author mhanna
* @version 0.1
*/
public class DirectOutputTracker extends OutputTracker {
    public <T> T getStorage( Stub<T> stub ) {
        Storage target = outputs.get(stub);
        if( target == null ) {
            target = StorageFactory.createStorage(stub);
            outputs.put(stub, target);
        }
        return (T)target;
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            threadLocalOutputStreams = new HashMap<Stub,Storage>();
            threadsToStorage.put( group, threadLocalOutputStreams );
        }

        for ( final Stub stub : outputs.keySet() ) {
            final Storage target = StorageFactory.createStorage(stub, createTempFile(stub));
            threadLocalOutputStreams.put(stub, target);
        }
    }
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        }
    }

    @Override
    public <T> T getStorage( final Stub<T> stub ) {
        Storage target;

        if (bypass) {
            target = outputs.get(stub);
            if( target == null ) {
                target = StorageFactory.createStorage(stub);
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            return null;

        final OutputMergeTask outputMergeTask = new OutputMergeTask();
        for( Map.Entry<Stub,Storage> entry: threadLocalOutputStreams.entrySet() ) {
            final Stub stub = entry.getKey();
            final Storage storageEntry = entry.getValue();

            storageEntry.close();
            outputMergeTask.addMergeOperation(getTargetStream(stub), storageEntry);
        }

//        logger.info("Closing " + Thread.currentThread().getId() + " => " + threadLocalOutputStreams);
        threadLocalOutputStreams.clear();
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Related Classes of org.broadinstitute.gatk.engine.io.storage.Storage

  • org.broadinstitute.gatk.engine.io.DirectOutputTracker
  • org.broadinstitute.gatk.engine.io.ThreadGroupOutputTracker
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