vdj_pipe::Composition_stats Class Reference

#include <composition_stats_step.hpp>

Inheritance diagram for vdj_pipe::Composition_stats:

Collaboration diagram for vdj_pipe::Composition_stats:

Public Member Functions
	VDJ_PIPE_STATIC_STRING_METHOD (comment,"calculate composition statistics of sequencing reads") VDJ_PIPE_STATIC_STRING_METHOD(description
based on trimmed reads	Composition_stats (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::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

Private Types
typedef boost::array< unsigned, 5 >	letter_counts
typedef std::vector< letter_counts >	counts_vector

Private Member Functions
void	write_composition () const
void	write_gc_hist () const

Private Attributes
counts_vector	cv_
Histogram_1d	gch_
std::string	comp_
std::string	gc_hist_

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 Typedef Documentation

typedef std::vector<letter_counts> vdj_pipe::Composition_stats::counts_vector

private

typedef boost::array<unsigned, 5> vdj_pipe::Composition_stats::letter_counts

private

Constructor & Destructor Documentation

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

Member Function Documentation

void vdj_pipe::Composition_stats::finish

(

)

void vdj_pipe::Composition_stats::run

(

)

vdj_pipe::Composition_stats::VDJ_PIPE_STATIC_STRING_METHOD	(	comment	,
		"calculate composition statistics of sequencing reads"
	)

void vdj_pipe::Composition_stats::write_composition ( ) const

private

void vdj_pipe::Composition_stats::write_gc_hist ( ) const

private

Member Data Documentation

std::string vdj_pipe::Composition_stats::comp_

private

counts_vector vdj_pipe::Composition_stats::cv_

private

std::string vdj_pipe::Composition_stats::gc_hist_

private

Histogram_1d vdj_pipe::Composition_stats::gch_

private

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

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