C++ (Cpp) mergeCigar示例

示例#1

文件： Allele.cpp 项目： Chunhsuan/freebayes

// combines the two alleles into a complex variant, updates important data
void Allele::mergeAllele(const Allele& newAllele, AlleleType newType) {
    //cout << stringForAllele(*this) << endl << stringForAllele(newAllele) << endl;
    type = newType;
    alternateSequence += newAllele.alternateSequence;
    length += newAllele.length; // hmmm
    basesRight = newAllele.basesRight;
    baseQualities.insert(baseQualities.end(), newAllele.baseQualities.begin(), newAllele.baseQualities.end());
    currentBase = base();
    // XXX note that we don't add Q values for intermingled gaps in combined alleles
    if (newAllele.type != ALLELE_REFERENCE) {
        quality = min(newAllele.quality, quality);
        lnquality = max(newAllele.lnquality, lnquality);
        //quality = minQuality(baseQualities);
        //lnquality = log(quality);
    } else {
        quality = averageQuality(baseQualities);
        lnquality = log(quality);
        basesRight += newAllele.referenceLength;
    }
    if (newAllele.type != ALLELE_REFERENCE) {
        repeatRightBoundary = newAllele.repeatRightBoundary;
    }
    cigar = mergeCigar(cigar, newAllele.cigar);
    referenceLength = referenceLengthFromCigar();
    //cout << stringForAllele(*this) << endl << endl;
}

示例#2

文件： Allele.cpp 项目： ekg/freebayes

// combines the two alleles into a complex variant, updates important data
void Allele::mergeAllele(const Allele& newAllele, AlleleType newType) {
    //cerr << stringForAllele(*this) << endl << stringForAllele(newAllele) << endl;
    type = newType;
    alternateSequence += newAllele.alternateSequence;
    length += newAllele.length; // hmmm
    basesRight = newAllele.basesRight;
    baseQualities.insert(baseQualities.end(), newAllele.baseQualities.begin(), newAllele.baseQualities.end());
    currentBase = base();
    quality = averageQuality(baseQualities);
    lnquality = phred2ln(quality);
    basesRight += newAllele.referenceLength;
    if (newAllele.type != ALLELE_REFERENCE) {
        repeatRightBoundary = newAllele.repeatRightBoundary;
    }
    cigar = mergeCigar(cigar, newAllele.cigar);
    referenceLength = referenceLengthFromCigar();
}