Examples of org.broadinstitute.gatk.engine.traversals.TraversalEngine.traverse()

Package org.broadinstitute.gatk.engine.traversals

Class org.broadinstitute.gatk.engine.traversals.TraversalEngine

Examples of org.broadinstitute.gatk.engine.traversals.TraversalEngine.traverse()

org.broadinstitute.gatk.engine.traversals.TraversalEngine.traverse()
this method must be implemented by all traversal engines @param walker the walker to run with @param dataProvider the data provider that generates data given the shard @param sum the accumulator @return an object of the reduce type

                    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();

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            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();

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                }
                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();

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