vdj_pipe
pipeline for processing DNA sequence data
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Look for external MIDs in FASTA/Q description lines. More...
#include <external_mid_inline.hpp>
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_ |
Look for external MIDs in FASTA/Q description lines.
vdj_pipe::External_mid_inline::External_mid_inline | ( | Vm_access_single const & | vma, |
boost::property_tree::ptree const & | pt, | ||
Pipe_environment & | pe | ||
) |
void vdj_pipe::External_mid_inline::run | ( | ) |