vdj_pipe
pipeline for processing DNA sequence data
pipe_paired_emid_read.hpp
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1 
7 #ifndef PIPE_PAIRED_EMID_READ_HPP_
8 #define PIPE_PAIRED_EMID_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 class Parser_fastq;
18 
22 public:
23  struct Err : public base_exception {};
25  void run();
26  Pipe_environment const& pe() const {return pe_;}
27 
28 private:
31 
32  void process_fastq(Seq_file_entry const& sfe);
33  void process_fasta_qual(Seq_file_entry const& sfe);
34 
35  void store_records(
36  Parser_fastq& psf,
37  Parser_fastq& psr,
38  Parser_fastq& pmf,
39  Parser_fastq& pmr
40  );
41 };
42 
43 }//namespace vdj_pipe
44 #endif /* PIPE_PAIRED_EMID_READ_HPP_ */
Pipe_environment pe_
Definition: pipe_paired_emid_read.hpp:30
Vm_access_paired_emid vma_
Definition: pipe_paired_emid_read.hpp:29
Parser for FASTQ files.
Definition: parser_fastq.hpp:19
Access to value map for paired eMID read pipeline and processing steps.
Definition: value_map_access_paired.hpp:145
Main namespace of vdj_pipe library.
Definition: keywords_variable.hpp:11
Definition: pipe_environment.hpp:26
Definition: pipe_paired_emid_read.hpp:23
#define VDJ_PIPE_DECL
Definition: config.hpp:23
Definition: sequence_file_entry.hpp:26
Definition: exception.hpp:23
process paired reads with external MIDs
Definition: pipe_paired_emid_read.hpp:21
Pipe_environment const & pe() const
Definition: pipe_paired_emid_read.hpp:26
bpt::ptree ptree
Definition: processing_step_utils.hpp:19