RegionAnnotation
RegionAnnotations::TheHQRegion() const {
std::vector<RegionAnnotation> hqs_ = HQRegions();
if (hqs_.size() == 0)
return RegionAnnotation(holeNumber_, RegionTypeMap::ToIndex(HQRegion, types_), 0, 0, 0);
else if (hqs_.size() == 1)
return hqs_[0];
else assert(false && "Zmw has more than one HQRegion.");
}
bool HDFPulseWriter::WriteOneZmw(const SMRTSequence& seq,
const std::vector<RegionAnnotation>& regions)
{
if (not this->WriteOneZmw(seq)) {
return false;
}
if (HasRegions()) {
if (regions.size() == 0) {
std::vector<RegionAnnotation> fake = {
RegionAnnotation(seq.HoleNumber(), HQRegion, 0, 0, 0)};
return regionsWriter_->Write(fake);
} else {
return regionsWriter_->Write(regions);
}
}
return true;
}
std::vector<ReadInterval>
RegionAnnotations::SubreadIntervals(const DNALength wholeLength,
const bool byAdapter,
const bool byHQRegion) const {
std::vector<RegionAnnotation> inserts;
if (not byAdapter) {
inserts = Inserts();
} else {
if (Adapters().size() != 0) {
// Must have at least one adapter in order find inserts by adapter.
std::vector<DNALength> starts, ends;
starts.push_back(0);
for(auto adapter: Adapters()) {
assert(wholeLength >= static_cast<DNALength>(adapter.GetStart()) and
wholeLength >= static_cast<DNALength>(adapter.GetEnd())); // bug if fail assert
starts.push_back(adapter.GetEnd());
ends.push_back(adapter.GetStart());
}
ends.push_back(wholeLength);
for (size_t i = 0; i < starts.size(); i++) {
// Use adapter to infer subreads, read score considered unknown.
if (ends[i] > starts[i]) {
inserts.push_back(RegionAnnotation(holeNumber_, Insert, starts[i], ends[i], 0));
}
}
} // else no inserts can be found
}
std::vector<ReadInterval> ret;
for (auto insert: inserts) {
if (byHQRegion) {
if (HasHQRegion()) {
DNALength s = std::max(static_cast<UInt>(insert.GetStart()), HQStart());
DNALength e = std::min(static_cast<UInt>(insert.GetEnd()), HQEnd());
if (s < e) {
// subreads' read score = HQRegion score.
ret.push_back(ReadInterval(s, e, HQScore()));
}
} // else ret = {}
} else {
ret.push_back(ReadInterval(insert));
}
}
return ret;
}
