multiCollector.addAllLevelsToFile(file); if(file.getNumHistograms() == 0) {
multiCollector.addAllLevelsToFile(file); if(file.getNumHistograms() == 0) {
@Test() public void testRawBqDistributionWithSoftClips() throws IOException { final String input = TEST_DATA_DIR + "chrMReadsWithClips.sam"; final File outFile = File.createTempFile("test", ".TargetedMetrics_Coverage"); outFile.deleteOnExit(); final String[] args = new String[] { "TARGET_INTERVALS=" + singleIntervals, "INPUT=" + input, "OUTPUT=" + outFile.getAbsolutePath(), "REFERENCE_SEQUENCE=" + referenceFile, "LEVEL=ALL_READS", "AMPLICON_INTERVALS=" + singleIntervals, "SAMPLE_SIZE=" + 0 }; Assert.assertEquals(runPicardCommandLine(args), 0); final MetricsFile<TargetedPcrMetrics, Comparable<Integer>> output = new MetricsFile<>(); output.read(new FileReader(outFile)); Assert.assertEquals(output.getMetrics().size(), 1); for (final TargetedPcrMetrics metrics : output.getMetrics()) { Assert.assertEquals(metrics.TOTAL_READS, 2); } Assert.assertEquals(output.getNumHistograms(), 2); final Histogram<Comparable<Integer>> histogram = output.getAllHistograms().get(1); Assert.assertTrue(TestNGUtil.compareDoubleWithAccuracy(histogram.getSumOfValues(), 62,0.01)); Assert.assertTrue(TestNGUtil.compareDoubleWithAccuracy(histogram.get(32).getValue(), 52D, 0.01)); Assert.assertTrue(TestNGUtil.compareDoubleWithAccuracy(histogram.get(33).getValue(), 10D, 0.01)); }