File: BWTSearch.hpp

package info (click to toggle)
pbseqlib 5.3.5%2Bdfsg-4
  • links: PTS, VCS
  • area: main
  • in suites: bookworm
  • size: 7,020 kB
  • sloc: cpp: 77,250; python: 331; sh: 103; makefile: 41
file content (27 lines) | stat: -rw-r--r-- 1,097 bytes parent folder | download | duplicates (4) 
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
 
#ifndef _BLASR_BWT_SEARCH_HPP_
#define _BLASR_BWT_SEARCH_HPP_

#include <vector>

#include <alignment/bwt/BWT.hpp>
#include <alignment/datastructures/anchoring/AnchorParameters.hpp>
#include <alignment/datastructures/anchoring/MatchPos.hpp>
#include <pbdata/FASTASequence.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