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

Look for external MIDs in FASTA/Q description lines. More...

#include <external_mid_inline.hpp>

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Public Member Functions

 External_mid_inline (Vm_access_single const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe)
 
void run ()
 
- Public Member Functions inherited from vdj_pipe::detail::Step_base_single
void reset_access (Value_ids_single const &ids)
 
- 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_single
typedef Vm_access_single 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_single
 Step_base_single (vma_type const &vma, boost::property_tree::ptree const &pt, Pipe_environment const &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_single
Vm_access_single vma_
 

Detailed Description

Look for external MIDs in FASTA/Q description lines.


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