// 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;
}
// 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();
}