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
|
#ifndef _BLASR_ALIGNMENT_SET_TO_CMPH5_ADAPTER_HPP_
#define _BLASR_ALIGNMENT_SET_TO_CMPH5_ADAPTER_HPP_
#include <alignment/datastructures/alignment/ByteAlignment.h>
#include <alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp>
#include <alignment/datastructures/alignment/AlignmentCandidate.hpp>
#include <hdf/HDFCmpFile.hpp>
#include <pbdata/sam/AlignmentSet.hpp>
#include <pbdata/utils/SMRTReadUtils.hpp>
class RefGroupNameId
{
public:
std::string name;
unsigned int id;
RefGroupNameId()
{
id = 0;
name = "";
}
RefGroupNameId(std::string n, unsigned int i)
{
name = n;
id = i;
}
RefGroupNameId(const RefGroupNameId &rhs)
{
name = rhs.name;
id = rhs.id;
}
};
// number of zmws per SMRTCell for springfield: 163482
const unsigned int numZMWsPerMovieSpringField = 163482;
template <typename T_CmpFile>
class AlignmentSetToCmpH5Adapter
{
public:
// Map reference name to reference group (/RefGroup) name and ID.
std::map<std::string, RefGroupNameId> refNameToRefGroupNameandId;
std::map<std::string, unsigned int> knownMovies;
std::map<std::string, unsigned int> knownPaths;
unsigned int numAlignments;
std::map<std::string, int> refNameToRefInfoIndex;
void Initialize() { numAlignments = 0; }
template <typename T_Reference>
void StoreReferenceInfo(std::vector<T_Reference> &references, T_CmpFile &cmpFile);
unsigned int StoreMovieInfo(std::string movieName, T_CmpFile &cmpFile);
// Given a reference name, find whether there exists a refGroup
// (e.g. /ref000001) associated with it.
// If not, create a refGroup and update refNameToRefGroupNameandId.
// Finally, return its associated refGroup ID.
unsigned int StoreRefGroup(std::string refName, T_CmpFile &cmpFile);
unsigned int StorePath(std::string &path, T_CmpFile &cmpFile);
void RemoveGapsAtEndOfAlignment(AlignmentCandidate<> &alignment);
void StoreAlignmentCandidate(AlignmentCandidate<> &alignment, int alnSegment,
T_CmpFile &cmpFile, int moleculeNumber = -1, bool copyQVs = false);
void StoreAlignmentCandidateList(std::vector<AlignmentCandidate<> > &alignments,
T_CmpFile &cmpFile, int moleculeNumber = -1,
bool copyQVs = false);
void StoreAlignmentCandidate(AlignmentCandidate<> alignment, T_CmpFile &cmpFile)
{
StoreAlignmentCandidate(alignment, 0, cmpFile);
}
};
#include "AlignmentSetToCmpH5AdapterImpl.hpp"
#endif
|
