NVBIO
|
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 |
Definition at line 35 of file pe_analyzer.cpp.
|
inline |
Definition at line 53 of file pe_analyzer.h.
|
inline |
Definition at line 55 of file pe_analyzer.h.
|
inline |
Definition at line 54 of file pe_analyzer.h.
|
inline |
Definition at line 56 of file pe_analyzer.h.
|
inline |
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.
|
inline |
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.
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.