vdj_pipe::Qual_stats Class Reference

#include <quality_stats_step.hpp>

Inheritance diagram for vdj_pipe::Qual_stats:

Collaboration diagram for vdj_pipe::Qual_stats:

Public Member Functions
	VDJ_PIPE_STATIC_STRING_METHOD (comment,"calculate quality statistics of sequencing reads") VDJ_PIPE_STATIC_STRING_METHOD(description
based on trimmed reads	Qual_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::multi_array< std::size_t, 2 >	heat_map
typedef boost::array< double, 5 >	fractions

Private Member Functions
void	write_heat_map () const
void	write_qstats () const
void	write_meanq_hist () const
void	write_len_hist () const

Static Private Member Functions
static fractions const &	fracts ()

Private Attributes
heat_map	hm_
Histogram_1d	mqh_
Histogram_1d	lh_
std::string	out_hm_
std::string	out_qs_
std::string	out_mqh_
std::string	out_len_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 boost::array<double,5> vdj_pipe::Qual_stats::fractions

private

typedef boost::multi_array<std::size_t, 2> vdj_pipe::Qual_stats::heat_map

private

Constructor & Destructor Documentation

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

Member Function Documentation

void vdj_pipe::Qual_stats::finish

(

)

static fractions const& vdj_pipe::Qual_stats::fracts ( )

inlinestaticprivate

void vdj_pipe::Qual_stats::run

(

)

vdj_pipe::Qual_stats::VDJ_PIPE_STATIC_STRING_METHOD	(	comment	,
		"calculate quality statistics of sequencing reads"
	)

void vdj_pipe::Qual_stats::write_heat_map ( ) const

private

void vdj_pipe::Qual_stats::write_len_hist ( ) const

private

void vdj_pipe::Qual_stats::write_meanq_hist ( ) const

private

void vdj_pipe::Qual_stats::write_qstats ( ) const

private

Member Data Documentation

heat_map vdj_pipe::Qual_stats::hm_

private

Histogram_1d vdj_pipe::Qual_stats::lh_

private

Histogram_1d vdj_pipe::Qual_stats::mqh_

private

std::string vdj_pipe::Qual_stats::out_hm_

private

std::string vdj_pipe::Qual_stats::out_len_hist_

private

std::string vdj_pipe::Qual_stats::out_mqh_

private

std::string vdj_pipe::Qual_stats::out_qs_

private

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

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