Package net.sf.picard.sam

Examples of net.sf.picard.sam.SamFileValidator$MaxOutputExceededException


    CramHeader cramHeader = iterator.getCramHeader();
    iterator.close();

    ProgressLogger progress = new ProgressLogger(log, 100000,
        "Validated Read");
    SamFileValidator v = new SamFileValidator(new PrintWriter(System.out),
        1);
    List<SAMValidationError.Type> errors = new ArrayList<SAMValidationError.Type>();
    errors.add(Type.MATE_NOT_FOUND);
//    errors.add(Type.MISSING_TAG_NM);
    v.setErrorsToIgnore(errors);
    v.init(referenceSequenceFile, cramHeader.samFileHeader);
    v.validateSamRecords(new SAMIterator.CramFileIterable(
        params.cramFile, referenceSequenceFile),
        cramHeader.samFileHeader);
    log.info("Elapsed seconds: " + progress.getElapsedSeconds());
  }
View Full Code Here

TOP

Related Classes of net.sf.picard.sam.SamFileValidator$MaxOutputExceededException

Copyright © 2018 www.massapicom. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.