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

#include <write_sequence_step.hpp>

Inheritance diagram for vdj_pipe::Write_seq:
Inheritance graph
[legend]
Collaboration diagram for vdj_pipe::Write_seq:
Collaboration graph
[legend]

Public Member Functions

 VDJ_PIPE_STATIC_STRING_METHOD (comment,"output sequences") Write_seq(Vm_access_single const &vm
 
void run ()
 
void finish ()
 
void summary (std::ostream &os) const
 
- 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
 

Public Attributes

boost::property_tree::ptree const & pt
 
boost::property_tree::ptree const Pipe_environmentpe
 

Private Attributes

File_ostream_variant fov_
 
std::size_t n_seq_
 
bool trim_
 
bool reverse_
 
bool skip_empty_
 

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
 
- 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 Attributes inherited from vdj_pipe::detail::Step_base_single
Vm_access_single vma_
 

Member Function Documentation

void vdj_pipe::Write_seq::finish ( )
inline
void vdj_pipe::Write_seq::run ( )
void vdj_pipe::Write_seq::summary ( std::ostream &  os) const
vdj_pipe::Write_seq::VDJ_PIPE_STATIC_STRING_METHOD ( comment  ,
"output sequences"   
) const

Member Data Documentation

File_ostream_variant vdj_pipe::Write_seq::fov_
private
std::size_t vdj_pipe::Write_seq::n_seq_
private
boost::property_tree::ptree const Pipe_environment& vdj_pipe::Write_seq::pe
boost::property_tree::ptree const& vdj_pipe::Write_seq::pt
bool vdj_pipe::Write_seq::reverse_
private
bool vdj_pipe::Write_seq::skip_empty_
private
bool vdj_pipe::Write_seq::trim_
private

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