/usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp is in libblasr-dev 0~20161219-2.
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 71 72 73 74 75 76 77 78 79 80 81 82 83 84 | #ifndef _BLASR_ALIGNMENT_SET_TO_CMPH5_ADAPTER_HPP_
#define _BLASR_ALIGNMENT_SET_TO_CMPH5_ADAPTER_HPP_
#include <utils/SMRTReadUtils.hpp> // pbdata
#include "../../../pbdata/sam/AlignmentSet.hpp"
#include <HDFCmpFile.hpp> // hdf
#include "datastructures/alignment/AlignmentCandidate.hpp"
#include "datastructures/alignment/ByteAlignment.h"
#include "../../algorithms/alignment/DistanceMatrixScoreFunction.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
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