// 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();
}
}
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();
}
// quality at a given reference position
const short Allele::currentQuality(void) const {
//cerr << readID << " " << position << "-" << position + length << " " << alternateSequence.size() << " vs " << baseQualities.size() << endl;
switch (this->type) {
case ALLELE_REFERENCE:
// should check a different way... this is wrong
// it will catch it all the time,
if (currentBase.size() > 1) {
return averageQuality(baseQualities);
} else {
int off = referenceOffset();
if (off < 0 || off > baseQualities.size()) {
return 0;
} else {
return baseQualities.at(off);
}
}
break;
case ALLELE_INSERTION:
case ALLELE_DELETION:
case ALLELE_SNP:
case ALLELE_MNP:
case ALLELE_COMPLEX:
return quality;
break;
}
return 0;
}
const bool Allele::masked(void) const {
// guard against uninitialized indelMask
if (indelMask.size() == 0)
return false;
if (genotypeAllele)
return false;
switch (this->type) {
case ALLELE_GENOTYPE:
return false;
break;
case ALLELE_REFERENCE:
return indelMask.at(referenceOffset());
break;
case ALLELE_SNP:
return indelMask.at(0);
break;
case ALLELE_INSERTION: // XXX presently these are masked by default...
case ALLELE_DELETION:
case ALLELE_MNP:
case ALLELE_COMPLEX:
case ALLELE_NULL:
return true;
break;
default:
break;
}
}
// quality at a given reference position
const short Allele::currentQuality(void) const {
switch (this->type) {
case ALLELE_REFERENCE:
assert(alternateSequence.size() == baseQualities.size());
assert(referenceOffset() >= 0);
TRY {
return baseQualities.at(referenceOffset());
} CATCH;
break;
case ALLELE_INSERTION:
case ALLELE_DELETION:
case ALLELE_SNP:
case ALLELE_MNP:
case ALLELE_COMPLEX:
return quality;
break;
}
}
