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nvbio::alndiff::PEAnalyzer Struct Reference

Detailed description

Definition at line 37 of file pe_analyzer.h.

#include <pe_analyzer.h>

Public Methods

 PEAnalyzer (Filter &filter, const bool id_check)
void push (const AlignmentPair &alnL, const AlignmentPair &alnR)
void generate_report (const char *aln_file_nameL, const char *aln_file_nameR, const char *report)
void flush ()
float mismatched () const
float different_ref () const
float distant () const
float discordant () const
uint32 filtered () const

Public Members

bool m_id_check
BooleanStats mapped
BooleanStats paired
BooleanStats unique
BooleanStats ambiguous
BooleanStats not_ambiguous
Histogram< 8 > paired_L_not_R_by_mapQ
Histogram< 8 > paired_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_ref12
Histogram< 8 > n_different_ref1
Histogram< 8 > n_different_ref2
Histogram< 8 > n_different_ref
Histogram< 8 > n_different_ref_unique
Histogram< 8 > n_different_ref_not_ambiguous
Histogram< 8 > n_distant12
Histogram< 8 > n_distant1
Histogram< 8 > n_distant2
Histogram< 8 > n_distant
Histogram< 8 > n_distant_unique
Histogram< 8 > n_distant_not_ambiguous
Histogram< 8 > n_discordant12
Histogram< 8 > n_discordant1
Histogram< 8 > n_discordant2
Histogram< 8 > n_discordant
Histogram< 8 > n_discordant_unique
Histogram< 8 > n_discordant_not_ambiguous
AlignmentStats al_stats
AlignmentStats distant_stats
AlignmentStats discordant_stats
Histogram2d< 12, 12 > sec_score_by_score_l
Histogram2d< 12, 12 > sec_score_by_score_r
Histogram2d< 16, 16 > sec_ed_by_ed_l
Histogram2d< 16, 16 > sec_ed_by_ed_r

Constructor & Destructor Documentation

nvbio::alndiff::PEAnalyzer::PEAnalyzer ( Filter filter,
const bool  id_check 

Definition at line 35 of file pe_analyzer.cpp.

Member Function Documentation

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

Definition at line 53 of file pe_analyzer.h.

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

Definition at line 55 of file pe_analyzer.h.

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

Definition at line 54 of file pe_analyzer.h.

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

Definition at line 56 of file pe_analyzer.h.

void nvbio::alndiff::PEAnalyzer::flush ( )

Definition at line 49 of file pe_analyzer.h.

void nvbio::alndiff::PEAnalyzer::generate_report ( const char *  aln_file_nameL,
const char *  aln_file_nameR,
const char *  report 

Definition at line 334 of file pe_analyzer.cpp.

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

Definition at line 51 of file pe_analyzer.h.

void nvbio::alndiff::PEAnalyzer::push ( const AlignmentPair alnL,
const AlignmentPair alnR 

Definition at line 43 of file pe_analyzer.cpp.

Member Data Documentation

AlignmentStats nvbio::alndiff::PEAnalyzer::al_stats

Definition at line 98 of file pe_analyzer.h.

BooleanStats nvbio::alndiff::PEAnalyzer::ambiguous

Definition at line 64 of file pe_analyzer.h.

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

Definition at line 71 of file pe_analyzer.h.

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

Definition at line 72 of file pe_analyzer.h.

AlignmentStats nvbio::alndiff::PEAnalyzer::discordant_stats

Definition at line 100 of file pe_analyzer.h.

AlignmentStats nvbio::alndiff::PEAnalyzer::distant_stats

Definition at line 99 of file pe_analyzer.h.

Filter& nvbio::alndiff::PEAnalyzer::m_filter

Definition at line 58 of file pe_analyzer.h.

bool nvbio::alndiff::PEAnalyzer::m_id_check

Definition at line 59 of file pe_analyzer.h.

BooleanStats nvbio::alndiff::PEAnalyzer::mapped

Definition at line 61 of file pe_analyzer.h.

uint32 nvbio::alndiff::PEAnalyzer::n

Definition at line 74 of file pe_analyzer.h.

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

Definition at line 80 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_different_ref1

Definition at line 78 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_different_ref12

Definition at line 77 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_different_ref2

Definition at line 79 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_different_ref_not_ambiguous

Definition at line 82 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_different_ref_unique

Definition at line 81 of file pe_analyzer.h.

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

Definition at line 94 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_discordant1

Definition at line 92 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_discordant12

Definition at line 91 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_discordant2

Definition at line 93 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_discordant_not_ambiguous

Definition at line 96 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_discordant_unique

Definition at line 95 of file pe_analyzer.h.

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

Definition at line 87 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_distant1

Definition at line 85 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_distant12

Definition at line 84 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_distant2

Definition at line 86 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_distant_not_ambiguous

Definition at line 89 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::n_distant_unique

Definition at line 88 of file pe_analyzer.h.

uint32 nvbio::alndiff::PEAnalyzer::n_mismatched

Definition at line 75 of file pe_analyzer.h.

BooleanStats nvbio::alndiff::PEAnalyzer::not_ambiguous

Definition at line 65 of file pe_analyzer.h.

BooleanStats nvbio::alndiff::PEAnalyzer::paired

Definition at line 62 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::paired_L_not_R_by_mapQ

Definition at line 67 of file pe_analyzer.h.

Histogram<8> nvbio::alndiff::PEAnalyzer::paired_R_not_L_by_mapQ

Definition at line 68 of file pe_analyzer.h.

Histogram2d<16,16> nvbio::alndiff::PEAnalyzer::sec_ed_by_ed_l

Definition at line 105 of file pe_analyzer.h.

Histogram2d<16,16> nvbio::alndiff::PEAnalyzer::sec_ed_by_ed_r

Definition at line 106 of file pe_analyzer.h.

Histogram2d<12,12> nvbio::alndiff::PEAnalyzer::sec_score_by_score_l

Definition at line 102 of file pe_analyzer.h.

Histogram2d<12,12> nvbio::alndiff::PEAnalyzer::sec_score_by_score_r

Definition at line 103 of file pe_analyzer.h.

BooleanStats nvbio::alndiff::PEAnalyzer::unique

Definition at line 63 of file pe_analyzer.h.

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

Definition at line 69 of file pe_analyzer.h.

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

Definition at line 70 of file pe_analyzer.h.

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