Package picard.analysis

Examples of picard.analysis.RrbsSummaryMetrics


  }

  @Test
  public void chrMReads() throws Exception {
    final MetricsFile<RrbsSummaryMetrics, ?> metricsFile = getSummaryFile(CHR_M_SAM, CHR_M_REFERENCE, rootTestDir + "/READ_TEST", new ArrayList<String>());
    final RrbsSummaryMetrics metrics = metricsFile.getMetrics().get(0);
    Assert.assertEquals(metrics.READS_ALIGNED.intValue(), 5);
    Assert.assertEquals(metrics.NON_CPG_BASES.intValue(), 15);
    Assert.assertEquals(metrics.NON_CPG_CONVERTED_BASES.intValue(), 11);
    Assert.assertEquals(metrics.PCT_NON_CPG_BASES_CONVERTED, 0.733333);
    Assert.assertEquals(metrics.CPG_BASES_SEEN.intValue(), 5);
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