Examples with StructuralVariantReadMetrics gridss.analysis.StructuralVariantReadMetrics used on opensource projects

Example 1 with StructuralVariantReadMetrics

use of gridss.analysis.StructuralVariantReadMetrics in project gridss by PapenfussLab.

the class ExtractSVReadsTest method should_write_metrics.

@Test
public void should_write_metrics() {
    createInput();
    ExtractSVReads extract = new ExtractSVReads();
    extract.INPUT = input;
    extract.OUTPUT = output;
    extract.METRICS_OUTPUT = new File(output.getAbsolutePath() + ".metrics");
    extract.setup(getHeader(), extract.INPUT);
    extract.acceptFragment(ImmutableList.of(Read(0, 1, "50M50S")), null);
    extract.finish();
    assertTrue(extract.METRICS_OUTPUT.exists());
    StructuralVariantReadMetrics metric = Iterators.getOnlyElement(Iterables.filter(MetricsFile.readBeans(extract.METRICS_OUTPUT), StructuralVariantReadMetrics.class).iterator(), null);
    assertEquals(1, metric.SOFT_CLIPPED_READS);
}