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

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

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        final TraverseReadsNano traverseReadsNano = new TraverseReadsNano(1);
        final DummyReadWalker walker = new DummyReadWalker();
        traverseReadsNano.initialize(engine, walker, null);

        for ( final Shard shard : dataSource.createShardIteratorOverAllReads(new ReadShardBalancer()) ) {
            final ReadShardDataProvider dataProvider = new ReadShardDataProvider(shard, engine.getGenomeLocParser(), dataSource.seek(shard), reference, new ArrayList<ReferenceOrderedDataSource>());
            traverseReadsNano.traverse(walker, dataProvider, 0);
            dataProvider.close();
        }

        Assert.assertEquals(engine.getCumulativeMetrics().getNumReadsSeen(), contigs.size() * numReadsPerContig);
        Assert.assertEquals(engine.getCumulativeMetrics().getNumIterations(), contigs.size() * numReadsPerContig);
    }
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        final TraverseReadsNano traverseReadsNano = new TraverseReadsNano(1);
        final DummyReadWalker walker = new DummyReadWalker();
        traverseReadsNano.initialize(engine, walker, null);

        for ( final Shard shard : dataSource.createShardIteratorOverAllReads(new ReadShardBalancer()) ) {
            final ReadShardDataProvider dataProvider = new ReadShardDataProvider(shard, engine.getGenomeLocParser(), dataSource.seek(shard), reference, new ArrayList<ReferenceOrderedDataSource>());
            traverseReadsNano.traverse(walker, dataProvider, 0);
            dataProvider.close();
        }

        Assert.assertEquals((long)engine.getCumulativeMetrics().getCountsByFilter().get(EveryTenthReadFilter.class.getSimpleName()), contigs.size() * numReadsPerContig / 10);
    }
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                    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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        for(Shard shard: shardStrategy) {
            if (shard == null) {
                fail("Shard == null");
            }

            ReadShardDataProvider dataProvider = new ReadShardDataProvider(shard,genomeLocParser,dataSource.seek(shard),null, Collections.<ReferenceOrderedDataSource>emptyList());
            accumulator = traversalEngine.traverse(countReadWalker, dataProvider, accumulator);
            dataProvider.close();
        }

        countReadWalker.onTraversalDone(accumulator);

        if (!(accumulator instanceof Long)) {
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Related Classes of org.broadinstitute.gatk.engine.datasources.providers.ReadShardDataProvider

  • org.broadinstitute.gatk.engine.executive.LinearMicroScheduler
  • org.broadinstitute.gatk.engine.ReadMetricsUnitTest
  • org.broadinstitute.gatk.engine.traversals.TraverseReadsUnitTest
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