string Allele::tojson(void) {
stringstream out;
if (!genotypeAllele) {
out << "{\"id\":\"" << readID << "\""
<< ",\"type\":\"" << typeStr() << "\""
<< ",\"length\":" << ((type == ALLELE_REFERENCE) ? 1 : length)
<< ",\"position\":" << position
<< ",\"strand\":\"" << (strand == STRAND_FORWARD ? "+" : "-") << "\"";
if (type == ALLELE_REFERENCE ) {
out << ",\"base\":\"" << alternateSequence.at(referenceOffset()) << "\""
//<< ",\"reference\":\"" << allele.referenceSequence.at(referenceOffset) << "\""
<< ",\"quality\":" << currentQuality();
} else {
out << ",\"base\":\"" << alternateSequence << "\""
//<< ",\"reference\":\"" << allele.referenceSequence << "\""
<< ",\"quality\":" << quality;
}
out << "}";
} else {
out << "{\"type\":\"" << typeStr() << "\"";
switch (type) {
case ALLELE_REFERENCE:
out << "}";
break;
default:
out << "\",\"length\":" << length
<< ",\"alt\":\"" << alternateSequence << "\"}";
break;
}
}
return out.str();
}
// 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();
}
}
const long double Allele::lncurrentQuality(void) const {
return phred2ln(currentQuality());
}
void Allele::setQuality(void) {
quality = currentQuality();
lnquality = phred2ln(quality);
}
