Java SAMRecord.getReadBases方法代码示例

import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
private int getNumClippedBasesAtStart(final SAMRecord read) {
    // compute total number of clipped bases (soft or hard clipped)
    // check for hard clips (never consider these bases):
    final Cigar c = read.getCigar();
    final CigarElement first = c.getCigarElement(0);

    int numStartClippedBases = 0;
    if (first.getOperator() == CigarOperator.H) {
        numStartClippedBases = first.getLength();
    }
    final byte[] unclippedReadBases = read.getReadBases();
    final byte[] unclippedReadQuals = read.getBaseQualities();

    // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative,
    // and may leave a string of Q2 bases still hanging off the reads.
    for (int i = numStartClippedBases; i < unclippedReadBases.length; i++) {
        if (unclippedReadQuals[i] < PairHMMIndelErrorModel.BASE_QUAL_THRESHOLD)
            numStartClippedBases++;
        else
            break;

    }

    return numStartClippedBases;
}
 

import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
/**
 * HACK TO CREATE GATKSAMRECORD BASED ONLY A SAMRECORD FOR TESTING PURPOSES ONLY
 * @param read
 */
public GATKSAMRecord(final SAMRecord read) {
    super(read.getHeader());
    setReferenceIndex(read.getReferenceIndex());
    setAlignmentStart(read.getAlignmentStart());
    mReadNameLength = (short)read.getReadNameLength();
    setMappingQuality(read.getMappingQuality());
    mCigarLength = read.getCigarLength();
    setFlags(read.getFlags());
    mReadLength = read.getReadLength();
    setMateReferenceIndex(read.getMateReferenceIndex());
    setMateAlignmentStart(read.getMateAlignmentStart());
    setInferredInsertSize(read.getInferredInsertSize());
    mRestOfBinaryData = null;

    super.setReadName(read.getReadName());
    super.setCigarString(read.getCigarString());
    super.setReadBases(read.getReadBases());
    super.setBaseQualities(read.getBaseQualities());

    SAMReadGroupRecord samRG = read.getReadGroup();
    clearAttributes();
    if (samRG != null) {
        GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
        setReadGroup(rg);
    }
    List<SAMTagAndValue> attributes = read.getAttributes();
    for(SAMTagAndValue tagAndValue : attributes) {
        setAttribute(tagAndValue.tag, tagAndValue.value);
    }
}
 

import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
public BAQCalculationResult(SAMRecord read, byte[] ref) {
    this(read.getBaseQualities(), read.getReadBases(), ref);
}
 

import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
/**
 * Creates a kmer sequence from a read's sequence.
 *
 * @param read the read to represent as a sequence of kmers.
 * @param kmerSize the kmer size.
 */
public KmerSequence(final SAMRecord read, final int kmerSize) {
    this(read.getReadBases(), kmerSize);
}