vdj_pipe
pipeline for processing DNA sequence data
sequence_merge.hpp
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1 
7 #ifndef SEQUENCE_MERGE_HPP_
8 #define SEQUENCE_MERGE_HPP_
9 #include <string>
10 #include <vector>
11 #include "vdj_pipe/config.hpp"
14 
15 namespace vdj_pipe{
16 
19 struct Merge_result {
23  sequence seq_;
24 
26  quality qual_;
27 
28  unsigned score_;
29 
30  std::string cigar_;
31 };
32 
35 VDJ_PIPE_DECL void merge(
36  std::string const& s1,
37  Seq_qual_record::quality const& qv1,
38  std::string const& s2, //in forward direction
39  Seq_qual_record::quality const& qv2, //in forward direction
40  const unsigned min_score,
41  Merge_result& mr
42 );
43 
44 
45 }//namespace vdj_pipe
46 #endif /* SEQUENCE_MERGE_HPP_ */
void merge(std::string const &s1, Seq_qual_record::quality const &qv1, std::string const &s2, Seq_qual_record::quality const &qv2, const unsigned min_score, Merge_result &mr)
Definition: sequence_merge.cpp:19
std::string cigar_
Definition: sequence_merge.hpp:30
Definition: sequence_record.hpp:35
unsigned score_
Definition: sequence_merge.hpp:28
const std::string s2
Definition: short_seq_map_run.cpp:18
Seq_record::sequence sequence
Definition: sequence_merge.hpp:20
const std::string s1
Definition: short_seq_map_run.cpp:17
Qual_record::quality quality
Definition: sequence_merge.hpp:21
Main namespace of vdj_pipe library.
Definition: keywords_variable.hpp:11
Definition: sequence_merge.hpp:19
#define VDJ_PIPE_DECL
Definition: config.hpp:23
std::string sequence
Definition: sequence_record.hpp:29
sequence seq_
Definition: sequence_merge.hpp:23
quality qual_
Definition: sequence_merge.hpp:26