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
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
|
#ifndef _BLASR_HDF_HDFZMWWriter_HPP_
#define _BLASR_HDF_HDFZMWWriter_HPP_
#include "../pbdata/libconfig.h"
#ifdef USE_PBBAM
#include "HDFWriterBase.hpp"
#include "BufferedHDFArray.hpp"
#include "BufferedHDF2DArray.hpp"
#include "../pbdata/SMRTSequence.hpp"
#include <pbbam/BamRecord.h>
class HDFBaseCallerWriter;
class HDFPulseCallerWriter;
class HDFZMWWriter: public HDFWriterBase {
friend class HDFBaseCallerWriter;
friend class HDFPulseCallerWriter;
public:
/// \name Constructors and Destructors
/// \{
HDFZMWWriter(const std::string & filename,
HDFGroup & parentGroup);
/// \params[in] filename
/// \params[in] parentGroup
/// \params[in] inPulseCalls, true if this ZMW is within PulseCalls.
/// \params[in] baseMap, base to channel index in H5.
HDFZMWWriter(const std::string & filename,
HDFGroup & parentGroup,
const bool inPulseCalls,
const std::map<char, size_t> & baseMap);
~HDFZMWWriter(void);
/// \}
/// \name Public Methods
/// \{
/// \returns true if this ZMW is within PulseCalls.
bool InPulseCalls(void) const;
/// \returns Whether or not to write BaseLineSigma
bool HasBaseLineSigma(void) const;
/// \note Write info of a SMRTSequence to ZMW,
/// (1) add number of pulses to NumEvent if InPulseCalls();
/// otherwise, add number of bases
/// (2) add zmw hole number (UInt) of the sequence as a UInt to HoleNumber,
/// (3) add hole status (unsigned char) to HoleStatus,
/// (4) add hole coordinate xy as (int16_t, int16_t) to HoleXY
bool WriteOneZmw(const PacBio::BAM::BamRecord & read);
bool WriteOneZmw(const SMRTSequence & read);
/// \brief Write fake datasets under /PulseCalls/ZMW
bool WriteFakeDataSets(void);
uint32_t NumZMWs(void) const {return arrayLength_;}
/// \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 Data
/// ZMW/NumEvent
BufferedHDFArray<uint32_t> numEventArray_;
/// ZMW/HoleNumber
BufferedHDFArray<unsigned int> holeNumberArray_;
/// ZMW/HoleStatus
BufferedHDFArray<unsigned char> holeStatusArray_;
/// ZMW/HoleXY
BufferedHDF2DArray<int16_t> holeXYArray_;
/// ZMW/BaseLineSigma
BufferedHDF2DArray<float> baseLineSigmaArray_;
/// ZMW group
HDFGroup zmwGroup_;
/// Parent group PulseCalls or BaseCalls
HDFGroup & parentGroup_;
/// Map 'ACGT' to channel indices, defined in /ScanData/RunInfo/BaseMap
std::map<char, size_t> baseMap_;
/// true if parent gropu is PulseCalls.
bool inPulseCalls_;
/// dataset (array) size.
uint32_t arrayLength_;
/// \}
private:
/// \name Private Methods
/// \{
/// \note Initialize child hdf groups under ZMW, including
/// NumEvent, HoleNumber, HoleStatus, HoleXY, and BaseLineSigma
/// \reutrns bool, whether or not child hdf groups successfully initialized.
bool InitializeChildHDFGroups(void);
/// \note Write number of bases to ZMW/NumEvent if not InPulseCalls();
/// Otherwise, write number of pulses.
bool _WriteNumEvent(const uint32_t numEvent);
/// \note Write HoleNumber
bool _WriteHoleNumber(const uint32_t holeNumber);
/// \note Write HoleXY
bool _WriteHoleXY(const int16_t holeX, const int16_t holeY);
/// \note Always write 'SEQUENCINGZMW' to HoleStatus
bool _WriteHoleStatus(const unsigned char holeStatus);
/// \note Write BaseLineSigma if it is required to write and exists in read
bool _WriteBaseLineSigma(const PacBio::BAM::BamRecord & read);
/// \note Add attributes to HoleNumber, HoleXY, HoleStatus, HoleXY and BaseLineSigma
void _WriteAttributes(void);
/// \}
};
#endif // end of #ifdef USE_PBBAM
#endif // end of #ifndef _BLASR_HDF_HDFZMWWriter_HPP_
|
