void BaseFile::CopyReadAt(uint32_t readIndex, SMRTSequence &read) {
assert(holeNumbers.size() > readIndex);
read.HoleNumber(holeNumbers[readIndex]);
if (holeXY.size() > 0) {
assert(holeXY.size() > readIndex);
read.HoleXY(holeXY[readIndex].xy[0],
holeXY[readIndex].xy[1]);
}
DSLength startPos = readStartPositions[readIndex];
DNALength readLength = readLengths[readIndex];
read.length = readLength;
read.Allocate(readLength);
if (baseCalls.size() > 0) {
assert(baseCalls.size() >= readLength + startPos);
CopyArray(baseCalls, startPos, readLength, read.seq);
}
if (qualityValues.size() > 0) {
assert(qualityValues.size() >= readLength + startPos);
CopyArray(qualityValues, startPos, readLength, read.qual.data);
}
if (basWidthInFrames.size() > 0) {
assert(basWidthInFrames.size() >= readLength + startPos);
CopyArray(basWidthInFrames, startPos, readLength, read.widthInFrames);
}
if (deletionQV.size() > 0) {
assert(deletionQV.size() >= readLength + startPos);
CopyArray(deletionQV, startPos, readLength, read.deletionQV.data);
}
if (deletionTag.size() > 0) {
assert(deletionTag.size() >= readLength + startPos);
CopyArray(deletionTag, startPos, readLength, read.deletionTag);
}
if (insertionQV.size() > 0) {
assert(insertionQV.size() >= readLength + startPos);
CopyArray(insertionQV, startPos, readLength, read.insertionQV.data);
}
if (substitutionQV.size() > 0) {
assert(substitutionQV.size() >= readLength + startPos);
CopyArray(substitutionQV, startPos, readLength, read.substitutionQV.data);
}
if (mergeQV.size() > 0) {
assert(mergeQV.size() >= readLength + startPos);
CopyArray(mergeQV, startPos, readLength, read.mergeQV.data);
}
if (substitutionTag.size() > 0) {
assert(substitutionTag.size() >= readLength + startPos);
CopyArray(substitutionTag, startPos, readLength, read.substitutionTag);
}
if (preBaseFrames.size() > 0) {
assert(preBaseFrames.size() >= readLength + startPos);
CopyArray(preBaseFrames, startPos, readLength, read.preBaseFrames);
}
}
void CreateSMRTSequence(SMRTSequence& smrt, Nucleotide* seq, int holeNumber, int start, int end)
{
int size = end - start;
smrt.seq = new Nucleotide[size];
memcpy(smrt.seq, seq, size * sizeof(Nucleotide));
smrt.length = size;
smrt.deleteOnExit = false;
smrt.HoleNumber(holeNumber);
smrt.SubreadStart(start);
smrt.SubreadEnd(end);
std::stringstream ss;
}
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;
}
void MakeVirtualRead(SMRTSequence & smrtRead,
const vector<SMRTSequence> & subreads)
{
assert(subreads.size() > 0);
DNALength hqStart = 0, hqEnd = 0;
for(auto subread: subreads) {
hqStart = min(DNALength(subread.SubreadStart()), hqStart);
hqEnd = max(DNALength(subread.SubreadEnd()), hqEnd);
}
smrtRead.Free();
smrtRead.Allocate(hqEnd);
memset(smrtRead.seq, 'N', sizeof(char) * hqEnd);
smrtRead.lowQualityPrefix = hqStart;
smrtRead.lowQualitySuffix = smrtRead.length - hqEnd;
smrtRead.highQualityRegionScore = subreads[0].highQualityRegionScore;
smrtRead.HoleNumber(subreads[0].HoleNumber());
stringstream ss;
ss << SMRTTitle(subreads[0].GetTitle()).MovieName() << "/" << subreads[0].HoleNumber();
smrtRead.CopyTitle(ss.str());
for (auto subread: subreads) {
memcpy(&smrtRead.seq[subread.SubreadStart()],
&subread.seq[0], sizeof(char) * subread.length);
}
}