vdj_pipe
pipeline for processing DNA sequence data
step_base.hpp
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1 
7 #ifndef STEP_BASE_HPP_
8 #define STEP_BASE_HPP_
9 #include <iosfwd>
10 #include "boost/property_tree/ptree_fwd.hpp"
11 #include "vdj_pipe/config.hpp"
13 #include "vdj_pipe/exception.hpp"
15 
16 namespace vdj_pipe{
17 class Pipe_environment;
18 
19 namespace detail{
20 
24 public:
27 
28  struct Err : public base_exception {};
29 
30  char delimiter() const {return delimiter_;}
31 
32  Step_base(
34  Pipe_environment const& pe
35  );
36 
37  void summary(std::ostream&) const {}
38 
39 private:
40  char delimiter_;
41 };
42 
43 }//namespace detail
44 }//namespace vdj_pipe
45 #endif /* STEP_BASE_HPP_ */
void summary(std::ostream &) const
Definition: step_base.hpp:37
Definition: sequence_record.hpp:35
char delimiter() const
Definition: step_base.hpp:30
Main namespace of vdj_pipe library.
Definition: keywords_variable.hpp:11
Definition: pipe_environment.hpp:26
Definition: step_base.hpp:23
#define VDJ_PIPE_DECL
Definition: config.hpp:23
Definition: step_base.hpp:28
char delimiter_
Definition: step_base.hpp:40
Seq_record::sequence seq_type
Definition: step_base.hpp:25
Qual_record::quality qual_type
Definition: step_base.hpp:26
std::string sequence
Definition: sequence_record.hpp:29
Definition: exception.hpp:23
bpt::ptree ptree
Definition: processing_step_utils.hpp:19