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pe_analyzer.h
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27 
28 #pragma once
29 
30 #include <nvbio-aln-diff/stats.h>
32 #include <nvbio-aln-diff/filter.h>
33 
34 namespace nvbio {
35 namespace alndiff {
36 
37 struct PEAnalyzer
38 {
39  PEAnalyzer(Filter& filter, const bool id_check);
40 
41  void push(
42  const AlignmentPair& alnL,
43  const AlignmentPair& alnR);
44 
45  void generate_report(const char* aln_file_nameL, const char* aln_file_nameR, const char* report);
46 
47  // flush any open files
48  //
49  void flush() { m_filter.flush(); }
50 
51  float mismatched() const { return float(n_mismatched)/float(n + n_mismatched); }
52 
53  float different_ref() const { return float(n_different_ref.count)/float(n); }
54  float distant() const { return float(n_distant.count)/float(n); }
55  float discordant() const { return float(n_discordant.count)/float(n); }
56  uint32 filtered() const { return m_filter.filtered(); }
57 
59  bool m_id_check;
60 
66 
73 
76 
83 
90 
97 
101 
104 
107 };
108 
109 } // namespace alndiff
110 } // namespace nvbio