vdj_pipe
pipeline for processing DNA sequence data
merge_paired_reads_step.hpp
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1 
7 #ifndef MERGE_PAIRED_READS_STEP_HPP_
8 #define MERGE_PAIRED_READS_STEP_HPP_
9 #include "vdj_pipe/config.hpp"
13 
14 namespace vdj_pipe{
15 
19 public:
21  VDJ_PIPE_STATIC_STRING_METHOD(name, "merge_paired")
22  VDJ_PIPE_STATIC_STRING_METHOD(category, "paired read")
23  VDJ_PIPE_STATIC_STRING_METHOD(comment, "merge forward and reverse reads")
24  VDJ_PIPE_STATIC_STRING_METHOD(description, "XXX")
25 
27  vma_type const& vma,
28  boost::property_tree::ptree const& pt,
30  );
31 
32  void run();
33  void finish() {}
34  void summary(std::ostream& os) const;
35 
36 private:
38  Val_id score_id_;
39  Val_id cigar_id_;
40  std::size_t n_merged_;
41  unsigned min_score_;
42  bool trimmed_;
43 };
44 
45 }//namespace vdj_pipe
46 #endif /* MERGE_PAIRED_READS_STEP_HPP_ */
Definition: sanitize_string.cpp:15
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
Access to value map for paired read pipeline and processing steps.
Definition: value_map_access_paired.hpp:16
Value_ids_single vis_
Definition: merge_paired_reads_step.hpp:37
Main namespace of vdj_pipe library.
Definition: keywords_variable.hpp:11
Definition: pipe_environment.hpp:26
Vm_access_paired vma_type
Definition: merge_paired_reads_step.hpp:20
#define VDJ_PIPE_DECL
Definition: config.hpp:23
unsigned min_score_
Definition: merge_paired_reads_step.hpp:41
std::size_t n_merged_
Definition: merge_paired_reads_step.hpp:40
Provides access to standard values for single read pipeline.
Definition: value_names.hpp:33
Val_id cigar_id_
Definition: merge_paired_reads_step.hpp:39
#define VDJ_PIPE_STATIC_STRING_METHOD(name, val)
Definition: keyword_struct_macro.hpp:12
Val_id score_id_
Definition: merge_paired_reads_step.hpp:38
Definition: step_base_paired.hpp:16
Definition: merge_paired_reads_step.hpp:18
bool trimmed_
Definition: merge_paired_reads_step.hpp:42
bpt::ptree ptree
Definition: processing_step_utils.hpp:19