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bnt.h
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27 
28 //
29 // NOTE: the code below is a derivative of bntseq.h, originally distributed
30 // under the MIT License, Copyright (c) 2008 Genome Research Ltd (GRL).
31 //
32 
33 #pragma once
34 
35 #include <nvbio/basic/types.h>
36 #include <string>
37 #include <vector>
38 #include <cstdio>
39 
40 namespace nvbio {
41 
42 struct BNTAnnData
43 {
44  BNTAnnData() : offset(0), len(0), n_ambs(0), gi(0) {}
45 
50 };
51 
52 struct BNTAnnInfo
53 {
54  std::string name;
55  std::string anno;
56 };
57 
58 struct BNTAmb
59 {
62  char amb;
63 };
64 
65 struct BNTSeq
66 {
67  BNTSeq() : l_pac(0), n_seqs(0), seed(0), n_holes(0) {}
68 
73  std::vector<BNTAnnInfo> anns_info; // n_seqs elements
74  std::vector<BNTAnnData> anns_data; // n_seqs elements
75  std::vector<BNTAmb> ambs; // n_holes elements
76 };
77 
78 struct BNTInfo
79 {
84 };
85 
87 {
88  virtual void set_info(const BNTInfo info) {}
89  virtual void read_ann(const BNTAnnInfo& info, BNTAnnData& data) {}
90  virtual void read_amb(const BNTAmb& amb) {}
91 };
92 
95 
96 void save_bns(const BNTSeq& bns, const char *prefix);
97 void load_bns(BNTSeq& bns, const char *prefix);
98 
99 void load_bns_info(BNTInfo& bns, const char *prefix);
100 void load_bns(BNTSeqLoader* bns, const char *prefix);
101 
102 } // namespace nvbio