Examples with OpticalDuplicatesArgumentCollection org.broadinstitute.hellbender.cmdline.argumentcollections.OpticalDuplicatesArgumentCollection used on opensource projects

Example 1 with OpticalDuplicatesArgumentCollection

use of org.broadinstitute.hellbender.cmdline.argumentcollections.OpticalDuplicatesArgumentCollection in project gatk by broadinstitute.

the class MarkDuplicatesSparkUnitTest method markDupesTest.

@Test(dataProvider = "md", groups = "spark")
public void markDupesTest(final String input, final long totalExpected, final long dupsExpected) throws IOException {
    JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    ReadsSparkSource readSource = new ReadsSparkSource(ctx);
    JavaRDD<GATKRead> reads = readSource.getParallelReads(input, null);
    Assert.assertEquals(reads.count(), totalExpected);
    SAMFileHeader header = readSource.getHeader(input, null);
    OpticalDuplicatesArgumentCollection opticalDuplicatesArgumentCollection = new OpticalDuplicatesArgumentCollection();
    final OpticalDuplicateFinder finder = opticalDuplicatesArgumentCollection.READ_NAME_REGEX != null ? new OpticalDuplicateFinder(opticalDuplicatesArgumentCollection.READ_NAME_REGEX, opticalDuplicatesArgumentCollection.OPTICAL_DUPLICATE_PIXEL_DISTANCE, null) : null;
    JavaRDD<GATKRead> markedReads = MarkDuplicatesSpark.mark(reads, header, MarkDuplicatesScoringStrategy.SUM_OF_BASE_QUALITIES, finder, 1);
    Assert.assertEquals(markedReads.count(), totalExpected);
    JavaRDD<GATKRead> dupes = markedReads.filter(GATKRead::isDuplicate);
    Assert.assertEquals(dupes.count(), dupsExpected);
}