bool HDFBaseCallsWriter::_WritePulseIndex(const SMRTSequence & read) {
if (HasPulseIndex()) {
if (read.copiedFromBam) {
const PacBio::BAM::BamRecord & record = read.bamRecord;
if (record.HasPulseCall()) {
const std::string & pulsecall = record.PulseCall();
std::vector<uint16_t> data(read.length, 0);
size_t indx = 0;
for(size_t i = 0; i < pulsecall.size(); i++) {
const char base = pulsecall[i];
if (base == 'A' or base == 'C' or base == 'G' or base == 'T') {
assert(indx < read.length);
data[indx] = static_cast<uint16_t>(i);
indx ++;
} else {
assert(base == 'a' or base == 'c' or base == 'g' or base == 't');
}
}
assert(indx == read.length);
pulseIndexArray_.Write(&data[0], read.length);
return true;
}
}
AddErrorMessage(std::string(PacBio::GroupNames::pulseindex) + " absent in read " + read.GetTitle());
return false;
}
return true;
}
bool HDFBaseCallsWriter::_WritePulseWidth(const SMRTSequence & read) {
if (HasPulseWidth()) {
if (read.widthInFrames == nullptr) {
AddErrorMessage(std::string(PacBio::GroupNames::widthinframes) + " absent in read " + read.GetTitle());
return false;
} else {
pulseWidthArray_.Write(read.widthInFrames, read.length);
return true;
}
}
return true;
}
bool HDFBaseCallsWriter::_WriteMergeQV(const SMRTSequence & read) {
if (HasMergeQV()) {
if (read.mergeQV.Empty()) {
AddErrorMessage(std::string(PacBio::GroupNames::mergeqv) + " absent in read " + read.GetTitle());
return false;
} else {
mergeQVArray_.Write(read.mergeQV.data, read.length);
return true;
}
}
return true;
}
bool HDFBaseCallsWriter::_WriteIPD(const SMRTSequence & read) {
if (HasIPD()) {
if (read.preBaseFrames == nullptr) {
AddErrorMessage(std::string(PacBio::GroupNames::prebaseframes) + " absent in read " + read.GetTitle());
return false;
} else {
ipdArray_.Write(read.preBaseFrames, read.length);
return true;
}
}
return true;
}
bool HDFBaseCallsWriter::_WriteSubstitutionTag(const SMRTSequence & read) {
if (HasSubstitutionTag()) {
if (read.substitutionTag == nullptr) {
AddErrorMessage(std::string(PacBio::GroupNames::substitutiontag) + " absent in read " + read.GetTitle());
return false;
} else {
substitutionTagArray_.Write(read.substitutionTag, read.length);
return true;
}
}
return true;
}