void ComputeSubreadIntervals(vector<SubreadInterval>* const intervals,
RegionTable& regionTable,
const unsigned holeNumber)
{
constexpr int RegionStart = RegionAnnotation::REGIONSTARTCOL;
constexpr int RegionEnd = RegionAnnotation::REGIONENDCOL;
// clear the input first
intervals->clear();
RegionAnnotations zmwRegions = regionTable[holeNumber];
// Has non-empty HQRegion or not?
if (not zmwRegions.HasHQRegion())
return;
//throw runtime_error("could not find HQRegion for ZMW " + to_string(holeNumber));
size_t hqStart = zmwRegions.HQStart();
size_t hqEnd = zmwRegions.HQEnd();
if (hqEnd <= hqStart)
return;
// this logic mirrors that in the C# codebase for DelimitedSeqRegions rather
// than what's in src/SubreadConverter.cpp for verification purposes
ReadInterval const * lastAdapter = nullptr;
bool prevIsAdapter = false;
size_t regStart = hqStart;
vector<ReadInterval> adapters = zmwRegions.AdapterIntervals();
for (size_t i = 0; i < adapters.size(); i++) {
ReadInterval adapter = adapters[i];
size_t adapterStart = adapter.start;
size_t adapterEnd = adapter.end;
if (adapterEnd < hqStart)
continue;
if (adapterStart > hqEnd)
break;
if (prevIsAdapter)
intervals->emplace_back(SubreadInterval(lastAdapter->end, adapterStart, true, true));
else if (regStart < adapterStart)
intervals->emplace_back(SubreadInterval(regStart, adapterStart, false, true));
lastAdapter = &adapters[i];
prevIsAdapter = true;
regStart = adapterEnd;
}
if (prevIsAdapter)
intervals->emplace_back(SubreadInterval(lastAdapter->end, hqEnd, true, false));
else if (regStart < hqEnd)
intervals->emplace_back(SubreadInterval(regStart, hqEnd, false, false));
}
// General functions.
bool LookupHQRegion(int holeNumber, RegionTable ®ionTable, int &start, int &end, int &score)
{
if (regionTable.HasHoleNumber(holeNumber)) {
RegionAnnotations zmwRegions = regionTable[holeNumber];
if (zmwRegions.HasHQRegion()) {
start = zmwRegions.HQStart();
end = zmwRegions.HQEnd();
score = zmwRegions.HQScore();
return true;
}
}
start = end = score = 0;
return false;
}
static
SubreadInterval ComputeSubreadIntervals(deque<SubreadInterval>* const intervals,
deque<SubreadInterval>* const adapters,
RegionTable& regionTable,
const unsigned holeNumber,
const size_t readLength)
{
constexpr int RegionStart = RegionAnnotation::REGIONSTARTCOL;
constexpr int RegionEnd = RegionAnnotation::REGIONENDCOL;
// clear the input first
intervals->clear();
adapters->clear();
// region annotations of a zmw
RegionAnnotations zmwRegions = regionTable[holeNumber];
// Has non-empty HQregion or not?
if (!zmwRegions.HasHQRegion())
return SubreadInterval(0, 0);
size_t hqStart = zmwRegions.HQStart();
size_t hqEnd = zmwRegions.HQEnd();
// Catch and repair 1-off errors in the HQ region
hqEnd = (hqEnd == readLength-1) ? readLength : hqEnd;
// Catch empty or invalid HQ regions and return empty
if (hqEnd <= hqStart)
return SubreadInterval(0, 0);
// adapter intervals of this zmw
vector<ReadInterval> adapterIntervals = zmwRegions.AdapterIntervals();
size_t subreadStart = hqStart;
bool adapterBefore = false;
for (size_t i = 0; i < adapterIntervals.size(); i++) {
size_t adapterStart = adapterIntervals[i].start;
size_t adapterEnd = adapterIntervals[i].end;
// if we're not in the HQRegion yet, skip ahead
if (hqStart > adapterEnd)
continue;
// if the adapter is beyond the HQRegion, we're done
if (hqEnd < adapterStart)
break;
// If the subread is greater than length=0, save it
if (subreadStart < adapterStart)
intervals->emplace_back(SubreadInterval(subreadStart, adapterStart, adapterBefore, true));
// Save the region of the adapter that overlaps the HQ region
adapters->emplace_back(SubreadInterval(MAX3(adapterStart, hqStart, subreadStart),
min(adapterEnd, hqEnd)));
subreadStart = adapterEnd;
adapterBefore = true;
}
// Save any region between the last adatper and the end of the HQ region as a subread
if (subreadStart < hqEnd)
intervals->emplace_back(SubreadInterval(subreadStart, hqEnd, adapterBefore, false));
return SubreadInterval(hqStart, hqEnd);
}
