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);
}
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