vdj_pipe::Ambiguous_window_filter Class Reference

#include <filter_step.hpp>

Inheritance diagram for vdj_pipe::Ambiguous_window_filter:

Collaboration diagram for vdj_pipe::Ambiguous_window_filter:

Public Member Functions
	VDJ_PIPE_STATIC_STRING_METHOD (comment,"Truncate reads to bring number of ambiguous bases below maximum") VDJ_PIPE_STATIC_STRING_METHOD(description
Find read interval at least min_len nucleotides long that has at most max_ambiguous ambiguous nucleotides Discard reads where such interval cannot be found If min_len is require that the whole read contains at most max_ambiguous ambiguous nucleotides	Ambiguous_window_filter (Vm_access_single const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe)
void	run ()
void	finish ()
Public Member Functions inherited from vdj_pipe::detail::Window_filter_base
void	summary (std::ostream &os) const
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
Find read interval at least min_len nucleotides long that has at most max_ambiguous ambiguous nucleotides Discard reads where such interval cannot be found If min_len is	zero

Private Attributes
std::size_t	min_len_
std::size_t	max_ambiguous_

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::Window_filter_base
	Window_filter_base (vma_type const &vma, boost::property_tree::ptree const &pt, Pipe_environment &pe)
void	trim (sequence_interval const &si)
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::Window_filter_base
std::size_t	nt_
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_

Constructor & Destructor Documentation

vdj_pipe::Ambiguous_window_filter::Ambiguous_window_filter	(	Vm_access_single const &	vma,
		boost::property_tree::ptree const &	pt,
		Pipe_environment &	pe
	)

Member Function Documentation

void vdj_pipe::Ambiguous_window_filter::finish ( )

inline

void vdj_pipe::Ambiguous_window_filter::run

(

)

vdj_pipe::Ambiguous_window_filter::VDJ_PIPE_STATIC_STRING_METHOD	(	comment	,
		"Truncate reads to bring number of ambiguous bases below maximum"
	)

Member Data Documentation

std::size_t vdj_pipe::Ambiguous_window_filter::max_ambiguous_

private

std::size_t vdj_pipe::Ambiguous_window_filter::min_len_

private

Find read interval at least min_len nucleotides long that has at most max_ambiguous ambiguous nucleotides Discard reads where such interval cannot be found If min_len is vdj_pipe::Ambiguous_window_filter::zero

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

• include/vdj_pipe/step/filter_step.hpp
• lib/filter_step.cpp