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
71
72
|
#ifndef _BLASR_HDF_CMP_EXPERIMENT_GROUP_HPP_
#define _BLASR_HDF_CMP_EXPERIMENT_GROUP_HPP_
#include <cstdint>
#include <map>
#include <set>
#include <vector>
#include <pbdata/Types.h>
#include <hdf/HDFArray.hpp>
#include <hdf/HDFCmpSupportedFields.hpp>
#include <hdf/HDFGroup.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, std::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<std::string> &fieldNames);
int Initialize(HDFGroup &refGroup, std::string experimentGroupName);
void Read();
HDFCmpExperimentGroup();
// Return reference alignment AlnArray size in KB.
UInt GetAlnArraySize();
};
#endif
|
