/usr/include/pbihdf/HDFCmpExperimentGroup.hpp is in libpbihdf-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 | #ifndef _BLASR_HDF_CMP_EXPERIMENT_GROUP_HPP_
#define _BLASR_HDF_CMP_EXPERIMENT_GROUP_HPP_
#include <map>
#include <vector>
#include <set>
#include <cstdint>
#include "Types.h"
#include "HDFGroup.hpp"
#include "HDFArray.hpp"
#include "HDFCmpSupportedFields.hpp"
class HDFCmpExperimentGroup {
public:
HDFCmpSupportedFields supportedFields;
HDFArray<unsigned int> startTimeOffset;
HDFArray<HalfWord> ipd;
HDFArray<HalfWord> preBaseFrames;
HDFArray<char> deletionTag;
HDFArray<char> substitutionTag;
HDFArray<UChar> qualityValue;
HDFArray<UChar> deletionQV;
HDFArray<UChar> insertionQV;
HDFArray<float> classifierQV;
// ClassifierQV date type is float in cmp.h5
HDFArray<UChar> substitutionQV;
HDFArray<UChar> mergeQV;
HDFArray<HalfWord> light;
HDFArray<HalfWord> widthInFrames;
HDFArray<HalfWord> pulseWidth;
HDFArray<unsigned int> startTime;
// StartFrame computed from Pulse metrics and Base metric
HDFArray<unsigned int> startTimeBase;
HDFArray<unsigned int> startTimePulse;
HDFArray<float> pkmid;
HDFArray<float> pkmax;
HDFArray<float> pkmean;
HDFArray<uint32_t> numPasses;
HDFArray<uint32_t> pulseIndex;
std::map<std::string, HDFData*> fields;
HDFGroup experimentGroup;
HDFArray<unsigned char> alignmentArray;
bool Create(HDFGroup &parent, string experimentGroupName);
void AddAlignment(std::vector<unsigned char> &alignment,
unsigned int &offsetBegin, unsigned int &offsetEnd);
// AddQVs and AddTags are like AddAlignment, but for QVs and Tags,
// respectively. They are responsible for initializing and writing to the
// correct member HDFArray, given a vector of values to write and the name
// of the QV or Tag
void AddQVs(const std::vector<UChar> &qualityValues, const std::string &fieldName,
unsigned int *offsetBegin, unsigned int *offsetEnd);
void AddTags(const std::vector<char> &qualityValues, const std::string &fieldName,
unsigned int *offsetBegin, unsigned int *offsetEnd);
int Initialize(HDFGroup &refGroup, std::string experimentGroupName,
std::set<string> &fieldNames);
int Initialize(HDFGroup &refGroup, std::string experimentGroupName);
void Read();
HDFCmpExperimentGroup();
// Return reference alignment AlnArray size in KB.
UInt GetAlnArraySize();
};
#endif
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