@Test(dataProvider = "validateBamFileTerminationData") public void validateBamFileTerminationTest(final File file, final SAMValidationError.Type errorType, final int numWarnings, final int numErrors) throws IOException { final SamFileValidator samFileValidator = new SamFileValidator(new PrintWriter(System.out), 8000); samFileValidator.validateBamFileTermination(file); Assert.assertEquals(samFileValidator.getErrorsByType().get(errorType).getValue(), 1.0); Assert.assertEquals(samFileValidator.getNumWarnings(), numWarnings); Assert.assertEquals(samFileValidator.getNumErrors(), numErrors); }
@Test public void testVerbose() throws IOException { final SAMRecordSetBuilder samBuilder = new SAMRecordSetBuilder(); for (int i = 0; i < 20; i++) { samBuilder.addFrag(String.valueOf(i), 1, i, false); } for (final SAMRecord record : samBuilder) { record.setProperPairFlag(true); } final StringWriter results = new StringWriter(); final SamFileValidator validator = new SamFileValidator(new PrintWriter(results), 8000); validator.setVerbose(true, 10); validator.validateSamFileVerbose(samBuilder.getSamReader(), null); final int lineCount = results.toString().split("\n").length; Assert.assertEquals(lineCount, 11); // 1 extra message added to indicate maximum number of errors Assert.assertEquals(validator.getNumErrors(), 6); Assert.assertEquals(validator.getNumWarnings(), 4); }
} else { if (validator.getNumErrors() == 0) { if (validator.getNumWarnings() > 0) { return ReturnTypes.WARNINGS.value(); // warnings but no errors } else { if (validator.getNumWarnings() > 0) { return ReturnTypes.ERRORS_WARNINGS.value(); // errors and warnings } else {
} else { if (validator.getNumErrors() == 0) { if (validator.getNumWarnings() > 0) { return ReturnTypes.WARNINGS.value(); // warnings but no errors } else { if (validator.getNumWarnings() > 0) { return ReturnTypes.ERRORS_WARNINGS.value(); // errors and warnings } else {