Examples with ContainsKmerReadFilterSpark org.broadinstitute.hellbender.tools.spark.sv.ContainsKmerReadFilterSpark used on opensource projects

Example 1 with ContainsKmerReadFilterSpark

use of org.broadinstitute.hellbender.tools.spark.sv.ContainsKmerReadFilterSpark in project gatk by broadinstitute.

the class PathSeqFilterSpark method doKmerFiltering.

@SuppressWarnings("unchecked")
private JavaRDD<GATKRead> doKmerFiltering(final JavaSparkContext ctx, final JavaRDD<GATKRead> reads) {
    final PipelineOptions options = getAuthenticatedGCSOptions();
    Input input = new Input(BucketUtils.openFile(KMER_LIB_PATH));
    Kryo kryo = new Kryo();
    kryo.setReferences(false);
    Set<SVKmer> kmerLibSet = (HopscotchSet<SVKmer>) kryo.readClassAndObject(input);
    return reads.filter(new ContainsKmerReadFilterSpark(ctx.broadcast(kmerLibSet), KMER_SIZE));
}

Example 2 with ContainsKmerReadFilterSpark

use of org.broadinstitute.hellbender.tools.spark.sv.ContainsKmerReadFilterSpark in project gatk by broadinstitute.

the class ContainsKmerReadFilterTest method testTest.

@Test(dataProvider = "sequenceStrings")
public void testTest(final String bases_in, final Boolean test_out) throws Exception {
    final JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    final ContainsKmerReadFilterSpark filter = new ContainsKmerReadFilterSpark(ctx.broadcast(kmerSet), kSize);
    final byte[] quals = bases_in.getBytes().clone();
    Arrays.fill(quals, (byte) 'I');
    SAMUtils.fastqToPhred(quals);
    GATKRead read_in = ArtificialReadUtils.createArtificialRead(bases_in.getBytes(), quals, "*");
    final Boolean test_i = filter.call(read_in);
    Assert.assertEquals(test_out, test_i);
}