/usr/include/blasr/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp is in libblasr-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 | #ifndef _BLASR_SAM_TO_ALIGNMENT_CANDIDATE_ADAPTER_HPP_
#define _BLASR_SAM_TO_ALIGNMENT_CANDIDATE_ADAPTER_HPP_
#include <map>
#include "sam/SAMAlignment.hpp"
#include "sam/SAMFlag.h"
#include "datastructures/alignment/AlignmentCandidate.hpp"
void InitializeCandidateFromSAM(SAMAlignment &sam,
AlignmentCandidate<> &candidate);
//
// Change a list of gap operations into a gap structure between
// blocks.
//
int ProcessGap(std::vector<int> &lengths, std::vector<char> &ops,
int &opIndex, int opEnd, blasr::GapList &gaps,
int &qAdvance, int &tAdvance);
inline bool IsClipping(char c) {
return (c == 'S' or c == 'H');
}
inline int IsSkipped(char c) {
return c == 'N';
}
//
//
// Returns true if the corresponding characters are assigned to each
// other in the alignment. This is either a match or a mismatch.
//
inline bool IsAssignChar(char c) {
return (c == 'M' or c == 'X' or c == '=');
}
int AdvancePastClipping(std::vector<int> &lengths,
std::vector<char> &ops,
int &opIndex,
int &numSoftClipped);
int AdvancePastSkipped(std::vector<int> &lengths,
std::vector<char> &ops,
int &opIndex);
int ProcessMatch(std::vector<int> &lengths, std::vector<char> &ops,
int &opIndex, int opEnd);
void CIGAROpsToBlocks(std::vector<int> &lengths, std::vector<char> &ops,
int cigarStart,
int cigarEnd,
AlignmentCandidate<> &aln);
int AdvancePosToAlignmentEnd(std::vector<char> &ops, int &pos);
int GetAlignedQueryLengthByCIGARSum(std::vector<char> &ops, std::vector<int> &lengths);
int GetAlignedReferenceLengthByCIGARSum(std::vector<char> &ops, std::vector<int> &lengths);
void CIGAROpsToBlocks(std::vector<int> &lengths, std::vector<char> &ops,
int &cigarPos,
int &cigarEnd,
int &qPos, int &tPos,
AlignmentCandidate<> &aln);
void ReverseAlignmentOperations(std::vector<int> &lengths, std::vector<char> &ops);
void SAMAlignmentsToCandidates(SAMAlignment &sam,
std::vector<FASTASequence> &referenceSequences,
std::map<std::string,int> & refNameToRefListIndex,
std::vector<AlignmentCandidate<> > &candidates,
bool parseSmrtTitle = false,
bool keepRefAsForward = true,
bool copyQVs = false);
#endif
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