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

#include <filter_step.hpp>

Inheritance diagram for vdj_pipe::Min_quality_filter:
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Collaboration diagram for vdj_pipe::Min_quality_filter:
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Public Member Functions

 VDJ_PIPE_STATIC_STRING_METHOD (comment,"discard reads that contain a quality score lower than minimal") Min_quality_filter(Vm_access_single const &vma
 
void run ()
 
void finish ()
 
- Public Member Functions inherited from vdj_pipe::detail::Filter_base
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 Types

typedef Qual_record::quality::value_type value_type
 

Private Attributes

value_type min_
 

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::Filter_base
 VDJ_PIPE_KEYWORD_STRUCT (kwds,(passed_name))
 
 Filter_base (vma_type const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe)
 
void pass (const bool b)
 
- 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::Filter_base
std::size_t nf_
 
Val_id pass_id_
 
- Protected Attributes inherited from vdj_pipe::detail::Step_base_single
Vm_access_single vma_
 

Member Typedef Documentation

Member Function Documentation

void vdj_pipe::Min_quality_filter::finish ( )
inline
void vdj_pipe::Min_quality_filter::run ( )
vdj_pipe::Min_quality_filter::VDJ_PIPE_STATIC_STRING_METHOD ( comment  ,
"discard reads that contain a quality score lower than minimal"   
) const

Member Data Documentation

value_type vdj_pipe::Min_quality_filter::min_
private
boost::property_tree::ptree const Pipe_environment& vdj_pipe::Min_quality_filter::pe
boost::property_tree::ptree const& vdj_pipe::Min_quality_filter::pt

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