/usr/include/pbdata/alignment/CmpAlignment.hpp is in libpbdata-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 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 | #ifndef DATASTRUCTURES_ALIGNMENT_CMP_ALIGNMENT_H_
#define DATASTRUCTURES_ALIGNMENT_CMP_ALIGNMENT_H_
#include <map>
#include <vector>
#include <string>
#include <iostream>
#include <assert.h>
#include <algorithm>
#include "Types.h"
#include "Enumerations.h"
class CmpAlignmentBase {
public:
//
// For use in referencing alignment sets. TODO: subclass.
//
PlatformId platformId;
int Z;
unsigned int index, readGroupId, movieId, refSeqId;
unsigned int expId, runId, panel;
unsigned int x, y;
unsigned int rcRefStrand;
unsigned int holeNumber;
unsigned int offsetBegin, offsetEnd;
unsigned int setNumber, strobeNumber, mapQV, nBackRead, nReadOverlap;
unsigned int subreadId;
unsigned int nMatch, nMismatch, nIns, nDel;
std::vector<unsigned char> alignmentArray;
std::vector<unsigned int> alignmentIndex;
static std::map<std::string,int> columnNameToIndex;
static bool initializedColumnNameToIndex;
std::map<std::string, std::vector<UChar> > fields;
unsigned int *GetAlignmentIndex();
int GetAlignmentIndexSize();
unsigned int GetAlignedStrand();
unsigned int GetRCRefStrand();
// synonym
unsigned int GetTStrand();
bool GetX(int &xp);
unsigned int GetAlignmentId();
unsigned int GetX();
unsigned int GetY();
unsigned int GetMovieId();
unsigned int GetAlnGroupId();
unsigned int GetReadGroupId();
unsigned int LookupColumnValue(const char * columnName);
void InitializeColumnNameToIndex(std::vector<std::string> &columnNames);
unsigned int GetHoleNumber();
unsigned int GetRefGroupId();
unsigned int GetRefSeqId();
unsigned int GetOffsetBegin();
unsigned int GetOffsetEnd();
unsigned int GetQueryStart();
unsigned int GetQueryEnd();
unsigned int GetRefStart();
unsigned int GetRefEnd();
unsigned int GetNMatch();
unsigned int GetNMismatch();
unsigned int GetNInsertions();
unsigned int GetNDeletions();
unsigned int GetMapQV();
unsigned int GetSubreadId();
unsigned int GetStrobeNumber();
unsigned int GetSetNumber();
CmpAlignmentBase(PlatformId platformIdP=Springfield);
void SetPlatformId(PlatformId platformIdP);
};
class CmpAlignment : public CmpAlignmentBase {
public:
int qStrand, tStrand;
int qStart, qLength;
int tStart, tLength;
//
// Default constructor just calls the base constructor to initialize platoformType
CmpAlignment(PlatformId pid=Springfield);
void StoreAlignmentIndex(unsigned int *alignmentIndexPtr, int alignmentIndexLength);
void StoreAlignmentArray(unsigned char* alignmentArrayPtr, int alignmentArrayLength);
template<typename T_Field>
void StoreField(std::string fieldName, T_Field* fieldValues, int length);
CmpAlignment &operator=(const CmpAlignment &rhs);
int operator<(const CmpAlignment &rhs) const;
};
#include "CmpAlignmentImpl.hpp"
#endif
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