@Test(dataProvider = "testOpticalDuplicateDetectionDataProvider")
public void testOpticalDuplicateDetection(
final File sam, final long expectedNumOpticalDuplicates) {
final File outputDir = IOUtil.createTempDir(TEST_BASE_NAME + ".", ".tmp");
outputDir.deleteOnExit();
final File outputSam = new File(outputDir, TEST_BASE_NAME + ".sam");
outputSam.deleteOnExit();
final File metricsFile = new File(outputDir, TEST_BASE_NAME + ".duplicate_metrics");
metricsFile.deleteOnExit();
// Run MarkDuplicates, merging the 3 input files, and either enabling or suppressing PG header
// record creation according to suppressPg.
final MarkDuplicates markDuplicates = new MarkDuplicates();
markDuplicates.setupOpticalDuplicateFinder();
markDuplicates.INPUT = CollectionUtil.makeList(sam.getAbsolutePath());
markDuplicates.OUTPUT = outputSam;
markDuplicates.METRICS_FILE = metricsFile;
markDuplicates.TMP_DIR = CollectionUtil.makeList(outputDir);
// Needed to suppress calling CommandLineProgram.getVersion(), which doesn't work for code not
// in a jar
markDuplicates.PROGRAM_RECORD_ID = null;
Assert.assertEquals(markDuplicates.doWork(), 0);
Assert.assertEquals(markDuplicates.numOpticalDuplicates(), expectedNumOpticalDuplicates);
TestUtil.recursiveDelete(outputDir);
}
