Examples of org.broadinstitute.gatk.engine.datasources.providers.ShardDataProvider

                    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();


            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.datasources.providers.ShardDataProvider

Related Classes of org.broadinstitute.gatk.engine.datasources.providers.ShardDataProvider