Examples of org.broadinstitute.gatk.engine.traversals.TraversalEngine

        this.outputTracker = outputTracker;
    }


    public Object call() {
        final Object traversalEngineKey = Thread.currentThread();
        final TraversalEngine traversalEngine = microScheduler.borrowTraversalEngine(traversalEngineKey);


        try {
            final long startTime = System.currentTimeMillis();


            // this is CRITICAL -- initializes output maps in this master thread,
            // so that any subthreads created by the traversal itself can access this map
            outputTracker.initializeStorage();


            Object accumulator = walker.reduceInit();
            final WindowMaker windowMaker = new WindowMaker(shard,microScheduler.getEngine().getGenomeLocParser(),
                    microScheduler.getReadIterator(shard),
                    shard.getGenomeLocs(),
                    microScheduler.engine.getSampleDB().getSampleNames()); // todo: microScheduler.engine is protected - is it okay to user it here?


            for(WindowMaker.WindowMakerIterator iterator: windowMaker) {
                final ShardDataProvider dataProvider = new LocusShardDataProvider(shard,iterator.getSourceInfo(),microScheduler.getEngine().getGenomeLocParser(),iterator.getLocus(),iterator,microScheduler.reference,microScheduler.rods);
                accumulator = traversalEngine.traverse(walker, dataProvider, accumulator);
                dataProvider.close();
            }


            windowMaker.close();
            outputMergeTask = outputTracker.closeStorage();

        Accumulator accumulator = Accumulator.create(engine,walker);


        boolean done = walker.isDone();
        int counter = 0;


        final TraversalEngine traversalEngine = borrowTraversalEngine(this);
        for (Shard shard : shardStrategy ) {
            if ( abortExecution() || done || shard == null ) // we ran out of shards that aren't owned
                break;


            if(shard.getShardType() == Shard.ShardType.LOCUS) {
                WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(),
                        getReadIterator(shard), shard.getGenomeLocs(), SampleUtils.getSAMFileSamples(engine));
                for(WindowMaker.WindowMakerIterator iterator: windowMaker) {
                    ShardDataProvider dataProvider = new LocusShardDataProvider(shard,iterator.getSourceInfo(),engine.getGenomeLocParser(),iterator.getLocus(),iterator,reference,rods);
                    Object result = traversalEngine.traverse(walker, dataProvider, accumulator.getReduceInit());
                    accumulator.accumulate(dataProvider,result);
                    dataProvider.close();
                    if ( walker.isDone() ) break;
                }
                windowMaker.close();
            }
            else {
                ShardDataProvider dataProvider = new ReadShardDataProvider(shard,engine.getGenomeLocParser(),getReadIterator(shard),reference,rods);
                Object result = traversalEngine.traverse(walker, dataProvider, accumulator.getReduceInit());
                accumulator.accumulate(dataProvider,result);
                dataProvider.close();
            }


            done = walker.isDone();

Examples of org.broadinstitute.gatk.engine.traversals.TraversalEngine

Related Classes of org.broadinstitute.gatk.engine.traversals.TraversalEngine