vdj_pipe
pipeline for processing DNA sequence data
Public Member Functions | List of all members
vdj_pipe::External_mid_infile Class Reference

Look for external MIDs in separate files. More...

#include <external_mid_infile.hpp>

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Public Member Functions

 External_mid_infile (vma_type const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe)
 
void run ()
 
- Public Member Functions inherited from vdj_pipe::detail::Step_base
char delimiter () const
 
 Step_base (boost::property_tree::ptree const &pt, Pipe_environment const &pe)
 
void summary (std::ostream &) const
 

Additional Inherited Members

- Public Types inherited from vdj_pipe::detail::Step_base_paired_emid
typedef Vm_access_paired_emid vma_type
 
- Public Types inherited from vdj_pipe::detail::Step_base
typedef Seq_record::sequence seq_type
 
typedef Qual_record::quality qual_type
 
- Public Types inherited from vdj_pipe::detail::External_mid_base
typedef Step_base::Err Err
 
- Protected Member Functions inherited from vdj_pipe::detail::Step_base_paired_emid
 Step_base_paired_emid (vma_type const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe)
 
- Protected Member Functions inherited from vdj_pipe::detail::External_mid_base
 VDJ_PIPE_KEYWORD_STRUCT (kwds,(fasta_path)(pairs_path)(value_name)(min_score)(max_mismatches)(require_best))
 
std::size_t mid_size () const
 
void find_mid (const boost::string_ref seq, Value_map &vm)
 
- Protected Attributes inherited from vdj_pipe::detail::Step_base_paired_emid
vma_type vma_
 

Detailed Description

Look for external MIDs in separate files.

Constructor & Destructor Documentation

vdj_pipe::External_mid_infile::External_mid_infile ( vma_type const &  vma,
boost::property_tree::ptree const &  pt,
Pipe_environment pe 
)

Member Function Documentation

void vdj_pipe::External_mid_infile::run ( )

The documentation for this class was generated from the following files: