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output_debug.h
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27 
28 #pragma once
29 
36 
37 #include <zlib/zlib.h>
38 
39 namespace nvbio {
40 namespace io {
41 
42 struct DebugOutput : public OutputFile
43 {
44  // structure that describes one read in the debug output format
45  struct DbgAlignment
46  {
49  uint32 alignment_pos; // if alignment_pos is 0, nothing else is written for this alignment
50 
51  // if alignment_pos is valid, struct Info follows
52  };
53 
54  struct DbgInfo
55  {
56  enum {
57  PAIRED = 1,
59  UNMAPPED = 4,
61  REVERSE = 16,
63  READ_1 = 64,
64  READ_2 = 128,
65  SECONDARY = 256,
66  QC_FAILED = 512,
67  DUPLICATE = 1024
68  };
69 
70  uint32 flag; // from enum above
72  // 8-bytes
77  // 12-bytes
81  // 16-bytes
86  // 20-bytes
89  // 24-bytes
90  };
91 
92 public:
94  ~DebugOutput();
95 
100  void process(struct HostOutputBatchSE& batch);
101 
106  void process(struct HostOutputBatchPE& batch);
107 
108  void close(void);
109 
110 private:
111  void output_alignment(gzFile& fp, const struct DbgAlignment& al, const struct DbgInfo& info);
112  void process_one_alignment(const AlignmentData& alignment, const AlignmentData& mate);
113  void process_one_mate(DbgAlignment& al,
114  DbgInfo& info,
115  const AlignmentData& alignment,
116  const AlignmentData& mate,
117  const uint32 mapq);
118 
119  // our file pointers
120  gzFile fp;
121  gzFile fp_opposite_mate;
122 };
123 
124 } // namespace io
125 } // namespace nvbio