static
void H5FilenamesFromBasH5(const string& basFileName,
vector<string>* const output)
{
HDFNewBasReader reader;
if (reader.Initialize(basFileName))
for (const auto& baxFileName : reader.GetBaxFileNames())
output->push_back(baxFileName);
else
output->push_back(basFileName);
}
std::vector<std::string> FileOfFileNames::Bas2Bax(std::string &basFN)
{
// There are two types of bas.h5 files.
// Before SMRT 2.0, bas.h5 files contain all the /PulseData data,
// in this case, return the bas.h5.
// After SMRT 2.0, bas.h5 files have been changed to only contain
// paths to bax.h5 files (in the /MultiPart/Parts group), while
// all base calls and QVs are in bax.h5 files. In this case,
// return path to the bax.h5 files. Assumption is that bax.h5
// files are in the same directory as bas.h5 file.
std::vector<std::string> baxFNs;
HDFNewBasReader reader;
if (reader.Initialize(basFN) != 0) {
baxFNs = reader.GetBaxFileNames();
} else {
baxFNs.push_back(basFN);
}
reader.Close();
return baxFNs;
}