Java SAMRecord.NO_ALIGNMENT_START属性代码示例

/**
 * Create an artificial read based on the parameters.  The cigar string will be *M, where * is the length of the read
 *
 * @param header         the SAM header to associate the read with
 * @param name           the name of the read
 * @param refIndex       the reference index, i.e. what chromosome to associate it with
 * @param alignmentStart where to start the alignment
 * @param length         the length of the read
 * @return the artificial read
 */
public static GATKSAMRecord createArtificialRead(SAMFileHeader header, String name, int refIndex, int alignmentStart, int length) {
    if ((refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart != SAMRecord.NO_ALIGNMENT_START) ||
            (refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_START))
        throw new ReviewedGATKException("Invalid alignment start for artificial read, start = " + alignmentStart);
    GATKSAMRecord record = new GATKSAMRecord(header);
    record.setReadName(name);
    record.setReferenceIndex(refIndex);
    record.setAlignmentStart(alignmentStart);
    List<CigarElement> elements = new ArrayList<CigarElement>();
    elements.add(new CigarElement(length, CigarOperator.characterToEnum('M')));
    record.setCigar(new Cigar(elements));
    record.setProperPairFlag(false);

    // our reads and quals are all 'A's by default
    byte[] c = new byte[length];
    byte[] q = new byte[length];
    for (int x = 0; x < length; x++)
        c[x] = q[x] = 'A';
    record.setReadBases(c);
    record.setBaseQualities(q);

    if (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
        record.setReadUnmappedFlag(true);
    }

    return record;
}
 

private boolean doNotTryToClean(GATKSAMRecord read) {
    return read.getReadUnmappedFlag() ||
            read.getNotPrimaryAlignmentFlag() ||
            read.getReadFailsVendorQualityCheckFlag() ||
            read.getMappingQuality() == 0 ||
            read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ||
            ConstrainedMateFixingManager.iSizeTooBigToMove(read, MAX_ISIZE_FOR_MOVEMENT) ||
            ReadUtils.is454Read(read) ||
            ReadUtils.isIonRead(read);
    // TODO -- it would be nice if we could use indels from 454/Ion reads as alternate consenses
}
 

@Override
public boolean filterOut(SAMRecord read) {
    return read.getReadUnmappedFlag() || read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START;
}
 

/**
 * Due to (unfortunate) multiple ways to indicate that read is unmapped allowed by SAM format
 * specification, one may need this convenience shortcut. Checks both 'read unmapped' flag and
 * alignment reference index/start.
 *
 * Our life would be so much easier if all sam files followed the specs. In reality,
 * sam files (including those generated by maq or bwa) miss headers altogether. When
 * reading such a SAM file, reference name is set, but since there is no sequence dictionary,
 * null is always returned for referenceIndex. Let's be paranoid here, and make sure that
 * we do not call the read "unmapped" when it has only reference name set with ref. index missing
 * or vice versa.
 *
 * @param r a non-null record
 * @return true if read is unmapped
 */
public static boolean isReadUnmapped(final SAMRecord r) {
    if ( r == null )
        throw new IllegalArgumentException("Read cannot be null");

    return r.getReadUnmappedFlag() ||
            !((r.getReferenceIndex() != null && r.getReferenceIndex() != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX ||
                    r.getReferenceName() != null && !r.getReferenceName().equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME)) &&
                    r.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START);

}