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#include <pbdata/utils/SMRTTitle.hpp>
/// Parse a Pacbio read name, it is a SMRTTitle, get movieName,
/// holeNumber, start and end, set isSMRTTitle to be true.
/// Otherwise, set isSMRTTitle to be false.
/// Two types of smrtTitles are supported:
/// movie/zmw/start_end --> start = start, end = end
/// movie/zmw/start_end/start2_end2 --> start = start+start2, end = start+end2
/// \param[in]: readName, a PacBio read name string.
SMRTTitle::SMRTTitle(const std::string& readName)
{
isSMRTTitle = false;
movieName = "";
holeNumber = 0;
start = end = 0;
std::vector<std::string> values;
ParseSeparatedList(readName, values, '/');
int numValues = values.size();
if (numValues == 3 or numValues == 4) {
movieName = values[0];
holeNumber = static_cast<UInt>(atoi(values[1].c_str()));
std::vector<std::string> offsets;
ParseSeparatedList(values[2], offsets, '_');
if (offsets.size() == 2) {
start = static_cast<DNALength>(atoi(offsets[0].c_str()));
end = static_cast<DNALength>(atoi(offsets[1].c_str()));
if (numValues == 3) {
isSMRTTitle = true;
} else if (numValues == 4) {
offsets.clear();
ParseSeparatedList(values[3], offsets, '_');
if (offsets.size() == 2) {
end = static_cast<DNALength>(start + atoi(offsets[1].c_str()));
start = static_cast<DNALength>(start + atoi(offsets[0].c_str()));
isSMRTTitle = true;
}
}
}
}
}
std::string SMRTTitle::ToString()
{
if (not isSMRTTitle) {
return "";
} else {
std::stringstream ss;
ss << movieName << "/" << holeNumber << "/" << start << "_" << end;
return ss.str();
}
}
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