vdj_pipe
pipeline for processing DNA sequence data
pipe_single_read.hpp
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1 
7 #ifndef PIPE_SINGLE_READ_HPP_
8 #define PIPE_SINGLE_READ_HPP_
9 #include <string>
10 #include "boost/property_tree/ptree_fwd.hpp"
11 #include "vdj_pipe/config.hpp"
14 
15 namespace vdj_pipe{
16 class Seq_file;
17 
20 class VDJ_PIPE_DECL Pipe_single_read {
21 public:
22  struct Err : public base_exception {};
23  explicit Pipe_single_read(boost::property_tree::ptree const& pt);
24  void run();
25  Pipe_environment const& pe() const {return pe_;}
26 
27 private:
28  Vm_access_single vma_;
29  Pipe_environment pe_;
30 
31  void process_fastq(Seq_file_entry const& sfe);
32  void process_fasta_qual(Seq_file_entry const& sfe);
33  void check() const;
34 };
35 
36 }//namespace vdj_pipe
37 #endif /* PIPE_SINGLE_READ_HPP_ */
Definition: pipe_single_read.hpp:22
Definition: value_map_access_single.hpp:16
Main namespace of vdj_pipe library.
Definition: sequence_file.hpp:14
Definition: pipe_environment.hpp:26
Definition: sequence_file_entry.hpp:26
Definition: pipe_single_read.hpp:20
Definition: exception.hpp:23