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// Author: Yuan Li
#ifndef _BLASR_HDF_HDFZMWMETRICSWriter_HPP_
#define _BLASR_HDF_HDFZMWMETRICSWriter_HPP_
#include <hdf/BufferedHDF2DArray.hpp>
#include <hdf/BufferedHDFArray.hpp>
#include <hdf/HDFWriterBase.hpp>
#include <pbdata/SMRTSequence.hpp>
class HDFBaseCallerWriter;
class HDFZMWMetricsWriter : public HDFWriterBase
{
friend class HDFBaseCallerWriter;
private:
/// \name Private variable
/// \{
HDFGroup& parentGroup_;
HDFGroup zmwMetricsGroup_;
/// HDF2DArray for writing average SNR within HQRegion.
BufferedHDF2DArray<float> hqRegionSNRArray_;
/// HDFArray for writing read raw accuracy prediction.
BufferedHDFArray<float> readScoreArray_;
/// HDFArray for writing Productivity
BufferedHDFArray<unsigned char> productivityArray_;
/// Map bases (e.g., ACGT) to indices
std::map<char, size_t> baseMap_;
int curRow_;
static const int SNRNCOLS = 4;
/// \}
public:
/// \name Constructors and Destructors
/// \{
HDFZMWMetricsWriter(const std::string& filename, HDFGroup& parentGroup,
const std::map<char, size_t>& baseMap);
~HDFZMWMetricsWriter(void);
/// \}
/// \name Public Methods
/// \{
/// \note Write info of a SMRTSequence to ZMWMetrics,
/// (1) add average signal to noise ratio in HQRegion to HQRegionSNR
/// (2) add read raw accuracy prediction to ReadScore
bool WriteOneZmw(const SMRTSequence& read);
/// \note Flushes all data from cache to disc.
void Flush(void);
/// \note Closes this zmw group as well as child hdf groups.
void Close(void);
/// \}
private:
/// \name Private Methods
/// \{
/// \note Initialize child hdf groups under ZMWMetrics, including
/// HQRegionSNR and ReadScore
/// \reutrns bool, whether or not child hdf groups successfully initialized.
bool InitializeChildHDFGroups(void);
/// \note Write Attributes.
bool WriteAttributes(void);
/// \}
};
#endif
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