Package org.broadinstitute.gatk.engine.datasources.providers

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

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        traverseLociNano.initialize(engine, walker, null);

        for ( final Shard shard : dataSource.createShardIteratorOverAllReads(new LocusShardBalancer()) ) {
            final WindowMaker windowMaker = new WindowMaker(shard, genomeLocParser, dataSource.seek(shard), shard.getGenomeLocs(), samples);
            for ( WindowMaker.WindowMakerIterator window : windowMaker ) {
                final LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, shard.getReadProperties(), genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>());
                traverseLociNano.traverse(walker, dataProvider, 0);
                dataProvider.close();
            }
            windowMaker.close();
        }

        //dataSource.close();
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        traverseActiveRegions.initialize(engine, walker, null);

        for ( final Shard shard : dataSource.createShardIteratorOverIntervals(new GenomeLocSortedSet(genomeLocParser, intervals), new ActiveRegionShardBalancer()) ) {
            final WindowMaker windowMaker = new WindowMaker(shard, genomeLocParser, dataSource.seek(shard), shard.getGenomeLocs(), samples);
            for ( WindowMaker.WindowMakerIterator window : windowMaker ) {
                final LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, shard.getReadProperties(), genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>());
                traverseActiveRegions.traverse(walker, dataProvider, 0);
                dataProvider.close();
            }
            windowMaker.close();
        }

        Assert.assertEquals(engine.getCumulativeMetrics().getNumReadsSeen(), contigs.size() * numReadsPerContig);
 
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                    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();
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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();
            }
            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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        traverseActiveRegions.initialize(engine, walker);
        List<LocusShardDataProvider> providers = new ArrayList<LocusShardDataProvider>();
        for (Shard shard : dataSource.createShardIteratorOverIntervals(new GenomeLocSortedSet(genomeLocParser, intervals), new ActiveRegionShardBalancer())) {
            for (WindowMaker.WindowMakerIterator window : new WindowMaker(shard, genomeLocParser, dataSource.seek(shard), shard.getGenomeLocs(), samples)) {
                providers.add(new LocusShardDataProvider(shard, shard.getReadProperties(), genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>()));
            }
        }

        return providers;
    }
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Related Classes of org.broadinstitute.gatk.engine.datasources.providers.LocusShardDataProvider

  • org.broadinstitute.gatk.engine.executive.LinearMicroScheduler
  • org.broadinstitute.gatk.engine.executive.ShardTraverser
  • org.broadinstitute.gatk.engine.ReadMetricsUnitTest
  • org.broadinstitute.gatk.engine.traversals.TraverseActiveRegionsUnitTest
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