Esempio n. 1
0
  @Test
  public void testCountsFromLocusTraversal() {
    final GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
    engine.setGenomeLocParser(genomeLocParser);

    final Collection<SAMReaderID> samFiles = new ArrayList<>();
    final SAMReaderID readerID = new SAMReaderID(testBAM, new Tags());
    samFiles.add(readerID);

    final SAMDataSource dataSource =
        new SAMDataSource(
            samFiles,
            new ThreadAllocation(),
            null,
            genomeLocParser,
            false,
            SAMFileReader.ValidationStringency.STRICT,
            null,
            null,
            new ValidationExclusion(),
            new ArrayList<ReadFilter>(),
            new ArrayList<ReadTransformer>(),
            false,
            (byte) 30,
            false,
            true);

    engine.setReadsDataSource(dataSource);
    final Set<String> samples = SampleUtils.getSAMFileSamples(dataSource.getHeader());

    final TraverseLociNano traverseLociNano = new TraverseLociNano(1);
    final DummyLocusWalker walker = new DummyLocusWalker();
    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();
    Assert.assertEquals(
        engine.getCumulativeMetrics().getNumReadsSeen(), contigs.size() * numReadsPerContig);
    Assert.assertEquals(
        engine.getCumulativeMetrics().getNumIterations(), contigs.size() * numReadsPerContig);
  }
Esempio n. 2
0
  @Test
  public void testFilteredCounts() {
    final GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
    engine.setGenomeLocParser(genomeLocParser);

    final Collection<SAMReaderID> samFiles = new ArrayList<>();
    final SAMReaderID readerID = new SAMReaderID(testBAM, new Tags());
    samFiles.add(readerID);

    final List<ReadFilter> filters = new ArrayList<>();
    filters.add(new EveryTenthReadFilter());

    final SAMDataSource dataSource =
        new SAMDataSource(
            samFiles,
            new ThreadAllocation(),
            null,
            genomeLocParser,
            false,
            SAMFileReader.ValidationStringency.STRICT,
            null,
            null,
            new ValidationExclusion(),
            filters,
            new ArrayList<ReadTransformer>(),
            false,
            (byte) 30,
            false,
            true);

    engine.setReadsDataSource(dataSource);

    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);
  }