v.validateSamFileSummary(reader, ReferenceSequenceFileFactory.getReferenceSequenceFile(params.reference)); log.info("Elapsed seconds: " + progress.getElapsedSeconds());
@Test public void testNonBarcodedWithCenter() throws Exception { final File outputBam = File.createTempFile("nonBarcodedDescriptionNonBI.", ".sam"); outputBam.deleteOnExit(); final int lane = 1; Assert.assertEquals(runPicardCommandLine(new String[]{ "BASECALLS_DIR=" + BASECALLS_DIR, "LANE=" + lane, "READ_STRUCTURE=25S8S25T", "OUTPUT=" + outputBam, "RUN_BARCODE=HiMom", "SAMPLE_ALIAS=HiDad", "SEQUENCING_CENTER=TEST_CENTER123", "LIBRARY_NAME=Hello, World" }), 0); final SamFileValidator validator = new SamFileValidator(new PrintWriter(System.out), 100); validator.validateSamFileSummary(SamReaderFactory.makeDefault().open(outputBam), null); IOUtil.assertFilesEqual(outputBam, new File(TEST_DATA_DIR, "nonBarcodedDescriptionNonBI.sam")); }
@Test(dataProvider = "molecularBarcodeData") public void testMolecularBarcodes(final String readStructure, final String[] umiTags, final String[] extraArgs, final String expectedSam, final int expectedReturn) throws Exception { final File outputBam = File.createTempFile("molecularBarcodeTest.", ".sam"); outputBam.deleteOnExit(); final int lane = 1; List<String> args = new ArrayList<>(CollectionUtil.makeList( "BASECALLS_DIR=" + BASECALLS_DIR, "LANE=" + lane, "READ_STRUCTURE=" + readStructure, "OUTPUT=" + outputBam, "RUN_BARCODE=HiMom", "SAMPLE_ALIAS=HiDad", "SEQUENCING_CENTER=BI", "LIBRARY_NAME=Hello, World")); if (umiTags != null) { for (final String umiTag : umiTags) { args.add("TAG_PER_MOLECULAR_INDEX=" + umiTag); } } if (extraArgs != null) { args.addAll(Arrays.asList(extraArgs)); } Assert.assertEquals(runPicardCommandLine(args), expectedReturn); if (expectedSam != null) { final SamFileValidator validator = new SamFileValidator(new PrintWriter(System.out), 100); validator.validateSamFileSummary(SamReaderFactory.makeDefault().open(outputBam), null); IOUtil.assertFilesEqual(outputBam, new File(TEST_DATA_DIR, expectedSam)); } }
private Histogram<String> executeValidationWithErrorIgnoring(final SamReader samReader, final ReferenceSequenceFile reference, final IndexValidationStringency stringency, final Collection<SAMValidationError.Type> ignoringError, final boolean skipMateValidation) throws IOException { final File outFile = File.createTempFile("validation", ".txt"); outFile.deleteOnExit(); final PrintWriter out = new PrintWriter(outFile); final SamFileValidator samFileValidator = new SamFileValidator(out, 8000); samFileValidator.setIndexValidationStringency(stringency).setErrorsToIgnore(ignoringError); samFileValidator.setSkipMateValidation(skipMateValidation); samFileValidator.validateSamFileSummary(samReader, reference); final LineNumberReader reader = new LineNumberReader(new FileReader(outFile)); if (reader.readLine().equals("No errors found")) { return new Histogram<>(); } final MetricsFile<MetricBase, String> outputFile = new MetricsFile<>(); outputFile.read(new FileReader(outFile)); Assert.assertNotNull(outputFile.getHistogram()); return outputFile.getHistogram(); }
final PrintWriter printWriter = new PrintWriter(outputStream)) { new SamFileValidator(printWriter, 100).validateSamFileSummary(samReader, null);
result = validator.validateSamFileSummary(samReader, reference); break; case VERBOSE:
result = validator.validateSamFileSummary(samReader, reference); break; case VERBOSE: