pipe_paired_read.hpp

Go to the documentation of this file.

#ifndef PIPE_PAIRED_READ_HPP_
#define PIPE_PAIRED_READ_HPP_
#include <string>
#include "boost/property_tree/ptree_fwd.hpp"
#include "vdj_pipe/config.hpp"
#include "vdj_pipe/exception.hpp"
#include "vdj_pipe/pipe_environment.hpp"
#include "vdj_pipe/value_map_access_paired.hpp"

namespace vdj_pipe{
class Seq_file;

class VDJ_PIPE_DECL Pipe_paired_read {
public:
   struct Err : public base_exception {};
   explicit Pipe_paired_read(boost::property_tree::ptree const& pt);
   void run();
   Pipe_environment const& pe() const {return pe_;}

private:
   Vm_access_paired vma_;
   Pipe_environment pe_;

   void check() const;
   void process_fastq(Seq_file_entry const& sfe);
   void process_fasta_qual(Seq_file_entry const& sfe);
   void store_records(
            Seq_qual_record const& r_fwd,
            Seq_qual_record const& r_rev
   );
};

}//namespace vdj_pipe
#endif /* PIPE_PAIRED_READ_HPP_ */