/usr/include/pbseq/alignment/algorithms/anchoring/BWTSearch.hpp is in libblasr-dev 0~20161219-1.
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 | #ifndef _BLASR_BWT_SEARCH_HPP_
#define _BLASR_BWT_SEARCH_HPP_
#include <vector>
#include "../../../pbdata/FASTASequence.hpp"
#include "../../bwt/BWT.hpp"
#include "../../datastructures/anchoring/MatchPos.hpp"
#include "../../datastructures/anchoring/AnchorParameters.hpp"
int MapReadToGenome(BWT & bwt,
FASTASequence & seq,
DNALength subreadStart, DNALength subreadEnd,
std::vector<ChainedMatchPos> &matchPosList,
AnchorParameters & params, int &numBasesAnchored,
std::vector<DNALength> & spv,
std::vector<DNALength> & epv);
int MapReadToGenome(BWT & bwt,
FASTASequence & seq,
DNALength start, DNALength end,
std::vector<ChainedMatchPos> & matchPosList,
AnchorParameters & params, int &numBasesAnchored);
template<typename T_MappingBuffers>
int MapReadToGenome(BWT & bwt,
FASTASequence & seq,
std::vector<ChainedMatchPos> &matchPosList,
AnchorParameters & params, int & numBasesAnchored,
T_MappingBuffers & mappingBuffers);
#include "BWTSearchImpl.hpp"
#endif
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