nvbio::alndiff::SEAnalyzer Struct Reference

Detailed description

Definition at line 37 of file se_analyzer.h.

#include <se_analyzer.h>

Public Methods
	SEAnalyzer (Filter &filter)
void	push (const Alignment &aln1, const Alignment &aln2)
void	generate_report (const char *aln_file_name1, const char *aln_file_name2, const char *report)
void	flush ()
float	mismatched () const
float	different_ref () const
float	distant () const
float	discordant () const
uint32	filtered () const

Public Members
Filter &	m_filter
BooleanStats	mapped
BooleanStats	unique
BooleanStats	ambiguous
BooleanStats	not_ambiguous
Histogram< 8 >	mapped_L_not_R_by_mapQ
Histogram< 8 >	mapped_R_not_L_by_mapQ
Histogram< 8 >	unique_L_not_R_by_mapQ
Histogram< 8 >	unique_R_not_L_by_mapQ
Histogram< 8 >	ambiguous_L_not_R_by_mapQ
Histogram< 8 >	ambiguous_R_not_L_by_mapQ
uint32	n
uint32	n_mismatched
Histogram< 8 >	n_different_ref
Histogram< 8 >	n_distant
Histogram< 8 >	n_discordant
AlignmentStats	al_stats
AlignmentStats	distant_stats
AlignmentStats	discordant_stats

Constructor & Destructor Documentation

nvbio::alndiff::SEAnalyzer::SEAnalyzer

(

Filter &

filter)

Definition at line 35 of file se_analyzer.cpp.

Member Function Documentation

float nvbio::alndiff::SEAnalyzer::different_ref ( ) const

inline

Definition at line 52 of file se_analyzer.h.

float nvbio::alndiff::SEAnalyzer::discordant ( ) const

inline

Definition at line 54 of file se_analyzer.h.

float nvbio::alndiff::SEAnalyzer::distant ( ) const

inline

Definition at line 53 of file se_analyzer.h.

uint32 nvbio::alndiff::SEAnalyzer::filtered ( ) const

inline

Definition at line 55 of file se_analyzer.h.

void nvbio::alndiff::SEAnalyzer::flush ( )

inline

Definition at line 49 of file se_analyzer.h.

void nvbio::alndiff::SEAnalyzer::generate_report	(	const char *	aln_file_name1,
		const char *	aln_file_name2,
		const char *	report
	)

Definition at line 170 of file se_analyzer.cpp.

float nvbio::alndiff::SEAnalyzer::mismatched ( ) const

inline

Definition at line 51 of file se_analyzer.h.

void nvbio::alndiff::SEAnalyzer::push	(	const Alignment &	aln1,
		const Alignment &	aln2
	)

Definition at line 42 of file se_analyzer.cpp.

Member Data Documentation

AlignmentStats nvbio::alndiff::SEAnalyzer::al_stats

Definition at line 78 of file se_analyzer.h.

BooleanStats nvbio::alndiff::SEAnalyzer::ambiguous

Definition at line 61 of file se_analyzer.h.

Histogram<8> nvbio::alndiff::SEAnalyzer::ambiguous_L_not_R_by_mapQ

Definition at line 68 of file se_analyzer.h.

Histogram<8> nvbio::alndiff::SEAnalyzer::ambiguous_R_not_L_by_mapQ

Definition at line 69 of file se_analyzer.h.

AlignmentStats nvbio::alndiff::SEAnalyzer::discordant_stats

Definition at line 80 of file se_analyzer.h.

AlignmentStats nvbio::alndiff::SEAnalyzer::distant_stats

Definition at line 79 of file se_analyzer.h.

Filter& nvbio::alndiff::SEAnalyzer::m_filter

Definition at line 57 of file se_analyzer.h.

BooleanStats nvbio::alndiff::SEAnalyzer::mapped

Definition at line 59 of file se_analyzer.h.

Histogram<8> nvbio::alndiff::SEAnalyzer::mapped_L_not_R_by_mapQ

Definition at line 64 of file se_analyzer.h.

Histogram<8> nvbio::alndiff::SEAnalyzer::mapped_R_not_L_by_mapQ

Definition at line 65 of file se_analyzer.h.

uint32 nvbio::alndiff::SEAnalyzer::n

Definition at line 71 of file se_analyzer.h.

Histogram<8> nvbio::alndiff::SEAnalyzer::n_different_ref

Definition at line 74 of file se_analyzer.h.

Histogram<8> nvbio::alndiff::SEAnalyzer::n_discordant

Definition at line 76 of file se_analyzer.h.

Histogram<8> nvbio::alndiff::SEAnalyzer::n_distant

Definition at line 75 of file se_analyzer.h.

uint32 nvbio::alndiff::SEAnalyzer::n_mismatched

Definition at line 72 of file se_analyzer.h.

BooleanStats nvbio::alndiff::SEAnalyzer::not_ambiguous

Definition at line 62 of file se_analyzer.h.

BooleanStats nvbio::alndiff::SEAnalyzer::unique

Definition at line 60 of file se_analyzer.h.

Histogram<8> nvbio::alndiff::SEAnalyzer::unique_L_not_R_by_mapQ

Definition at line 66 of file se_analyzer.h.

Histogram<8> nvbio::alndiff::SEAnalyzer::unique_R_not_L_by_mapQ

Definition at line 67 of file se_analyzer.h.

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

• E:/git/nvbio/nvbio-aln-diff/se_analyzer.h
• E:/git/nvbio/nvbio-aln-diff/se_analyzer.cpp