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#include "../pbdata/libconfig.h"
#ifdef USE_PBBAM
#include "HDFBaxWriter.hpp"
HDFBaxWriter::HDFBaxWriter(const std::string & filename,
const std::string & basecallerVersion,
const std::map<char, size_t>& baseMap,
const std::vector<PacBio::BAM::BaseFeature> & qvsToWrite,
const H5::FileAccPropList & fileAccPropList)
: HDFWriterBase(filename)
, fileaccproplist_(fileAccPropList)
, basecallsWriter_(nullptr)
, regionsWriter_(nullptr)
{
// open file
outfile_.Open(filename_, H5F_ACC_TRUNC, fileaccproplist_);
// Add PulseData group to the root group '/'
AddChildGroup(outfile_.rootGroup, pulseDataGroup_, PacBio::GroupNames::pulsedata);
if (basecallerVersion.empty()) {
AddErrorMessage("Base caller version must be specified.");
}
// Create a BaseCaller writer.
basecallsWriter_.reset(new HDFBaseCallsWriter(filename_, pulseDataGroup_, baseMap, basecallerVersion, qvsToWrite));
}
HDFBaxWriter::HDFBaxWriter(const std::string & filename,
const std::string & basecallerVersion,
const std::map<char, size_t>& baseMap,
const std::vector<PacBio::BAM::BaseFeature> & qvsToWrite,
const std::vector<std::string> & regionTypes,
const H5::FileAccPropList & fileAccPropList)
: HDFBaxWriter(filename, basecallerVersion, baseMap, qvsToWrite, fileAccPropList)
{
// Create a Regions writer.
regionsWriter_.reset(new HDFRegionsWriter(filename_, pulseDataGroup_, regionTypes));
}
HDFBaxWriter::~HDFBaxWriter(void) {
this->Close();
}
void HDFBaxWriter::Flush(void) {
basecallsWriter_->Flush();
if (HasRegions()) regionsWriter_->Flush();
}
std::vector<std::string> HDFBaxWriter::Errors(void) {
std::vector<std::string> errors = errors_;
for (auto error: basecallsWriter_->Errors())
errors.emplace_back(error);
if (HasRegions()) {
for (auto error: regionsWriter_->Errors())
errors.emplace_back(error);
}
return errors;
}
void HDFBaxWriter::Close(void) {
if (basecallsWriter_) basecallsWriter_.reset();
if (HasRegions() and regionsWriter_) regionsWriter_.reset();
outfile_.Close();
}
bool HDFBaxWriter::WriteOneZmw(const SMRTSequence & seq) {
return basecallsWriter_->WriteOneZmw(seq);
}
bool HDFBaxWriter::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;
}
bool HDFBaxWriter::WriteFakeDataSets() {
return basecallsWriter_->WriteFakeDataSets();
}
#endif // end of ifdef USE_PBBAM
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