/** * @deprecated use {@link #setIndexValidationStringency} instead */ @Deprecated public SamFileValidator setValidateIndex(final boolean validateIndex) { // The SamReader must also have IndexCaching enabled to have the index validated, return this.setIndexValidationStringency(validateIndex ? IndexValidationStringency.EXHAUSTIVE : IndexValidationStringency.NONE); }
/** * @deprecated use {@link #setIndexValidationStringency} instead */ @Deprecated public SamFileValidator setValidateIndex(final boolean validateIndex) { // The SamReader must also have IndexCaching enabled to have the index validated, return this.setIndexValidationStringency(validateIndex ? IndexValidationStringency.EXHAUSTIVE : IndexValidationStringency.NONE); }
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(); }
validator.setIndexValidationStringency(VALIDATE_INDEX ? IndexValidationStringency.EXHAUSTIVE : IndexValidationStringency.NONE);
validator.setIndexValidationStringency(VALIDATE_INDEX ? IndexValidationStringency.EXHAUSTIVE : IndexValidationStringency.NONE);