vdj_pipe
pipeline for processing DNA sequence data
write_sequence_step.hpp
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1 
7 #ifndef WRITE_SEQUENCE_STEP_HPP_
8 #define WRITE_SEQUENCE_STEP_HPP_
9 #include <iosfwd>
10 #include <string>
11 #include "boost/property_tree/ptree_fwd.hpp"
12 #include "boost/shared_ptr.hpp"
13 #include "vdj_pipe/config.hpp"
17 
18 namespace vdj_pipe{
19 
23 public:
24  VDJ_PIPE_STATIC_STRING_METHOD(name, "write_sequence")
25  VDJ_PIPE_STATIC_STRING_METHOD(category, "output")
27  comment,
28  "output sequences"
29  )
30  VDJ_PIPE_STATIC_STRING_METHOD(description, "XXX")
31 
32  Write_seq(
33  Vm_access_single const& vm,
36  );
37 
38  void run();
39  void finish() {}
40  void summary(std::ostream& os) const;
41 
42 private:
44  std::size_t n_seq_;
45  bool trim_;
46  bool reverse_;
48 };
49 
50 }//namespace vdj_pipe
51 #endif /* WRITE_SEQUENCE_STEP_HPP_ */
bool reverse_
Definition: write_sequence_step.hpp:46
Select output file based on variables in value map.
Definition: file_ostream_variant.hpp:27
Definition: write_sequence_step.hpp:22
void finish()
Definition: write_sequence_step.hpp:39
bool trim_
Definition: write_sequence_step.hpp:45
Definition: value_map_access_single.hpp:16
bool skip_empty_
Definition: write_sequence_step.hpp:47
Main namespace of vdj_pipe library.
Definition: keywords_variable.hpp:11
Definition: pipe_environment.hpp:26
#define VDJ_PIPE_DECL
Definition: config.hpp:23
#define VDJ_PIPE_STATIC_STRING_METHOD(name, val)
Definition: keyword_struct_macro.hpp:12
std::size_t n_seq_
Definition: write_sequence_step.hpp:44
Definition: step_base_single.hpp:16
bpt::ptree ptree
Definition: processing_step_utils.hpp:19
File_ostream_variant fov_
Definition: write_sequence_step.hpp:43