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#include <pbdata/utils/SMRTReadUtils.hpp>
void GetSMRTReadCoordinates(FASTQSequence &seq, int &x, int &y)
{
std::string str(seq.title, seq.titleLength);
std::vector<std::string> titleTokens;
Splice(str, "_", titleTokens);
x = y = -1;
for (size_t i = 0; i < titleTokens.size(); i++) {
if (titleTokens[i].size() > 1 && titleTokens[i][0] == 'x') {
x = atoi(&titleTokens[i].c_str()[1]);
}
if (titleTokens[i].size() > 1 && titleTokens[i][0] == 'y') {
y = atoi(&titleTokens[i].c_str()[1]);
}
}
assert("Could not parse a title to find an x coordinate" != 0 or x != -1);
assert("Could not parse a title to find a y coordiante" != 0 or y != -1);
}
void GetSpringfieldHoleNumberFromTitle(FASTQSequence &seq, unsigned int &holeNumber)
{
std::vector<std::string> titleTokens;
Splice(seq.title, "/", titleTokens);
if (titleTokens.size() < 2) {
return;
}
holeNumber = atoi(titleTokens[1].c_str());
}
bool ParsePBIReadName(std::string &readName, std::string &movieName, int &holeNumber)
{
std::vector<std::string> tokens;
ParseSeparatedList(readName, tokens, '/');
if (tokens.size() < 2) {
movieName = "";
holeNumber = 0;
return false;
} else {
movieName = tokens[0];
holeNumber = atoi(tokens[1].c_str());
return true;
}
}
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