vdj_pipe
pipeline for processing DNA sequence data
pipe_paired_read.hpp
Go to the documentation of this file.
1 
7 #ifndef PIPE_PAIRED_READ_HPP_
8 #define PIPE_PAIRED_READ_HPP_
9 #include <string>
10 #include "boost/property_tree/ptree_fwd.hpp"
11 #include "vdj_pipe/config.hpp"
12 #include "vdj_pipe/exception.hpp"
15 
16 namespace vdj_pipe{
17 class Seq_file;
18 
21 class VDJ_PIPE_DECL Pipe_paired_read {
22 public:
23  struct Err : public base_exception {};
24  explicit Pipe_paired_read(boost::property_tree::ptree const& pt);
25  void run();
26  Pipe_environment const& pe() const {return pe_;}
27 
28 private:
29  Vm_access_paired vma_;
30  Pipe_environment pe_;
31 
32  void check() const;
33  void process_fastq(Seq_file_entry const& sfe);
34  void process_fasta_qual(Seq_file_entry const& sfe);
35  void store_records(
36  Seq_qual_record const& r_fwd,
37  Seq_qual_record const& r_rev
38  );
39 };
40 
41 }//namespace vdj_pipe
42 #endif /* PIPE_PAIRED_READ_HPP_ */
Definition: pipe_paired_read.hpp:23
Access to value map for paired read pipeline and processing steps.
Definition: value_map_access_paired.hpp:16
Definition: sequence_record.hpp:77
Main namespace of vdj_pipe library.
Definition: sequence_file.hpp:14
Definition: pipe_environment.hpp:26
Definition: sequence_file_entry.hpp:26
Definition: exception.hpp:23
process paired reads with external MIDs
Definition: pipe_paired_read.hpp:21