// called prior to using the allele in analysis
void Allele::update(void) {
quality = currentQuality();
lnquality = phred2ln(quality);
if (type == ALLELE_REFERENCE) {
currentBase = string(1, *currentReferenceBase);
basesLeft = bpLeft + referenceOffset();
basesRight = bpRight - referenceOffset();
} else {
currentBase = base();
}
}
// 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();
}
// quality of subsequence of allele
const long double Allele::lnsubquality(int startpos, int len) const {
return phred2ln(subquality(startpos, len));
}
const long double Allele::lncurrentQuality(void) const {
return phred2ln(currentQuality());
}
const long double Allele::lnsubquality(const Allele& a) const {
return phred2ln(subquality(a));
}
void Allele::setQuality(void) {
quality = currentQuality();
lnquality = phred2ln(quality);
}
