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compute_thread.h
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27 
28 #pragma once
29 
33 #include <nvbio/basic/threads.h>
34 #include <map>
35 #include <string>
36 
37 namespace nvbio { namespace io { struct OutputFile; } }
38 
39 namespace nvbio {
40 namespace bowtie2 {
41 namespace cuda {
42 
43 struct InputThreadSE;
44 struct InputThreadPE;
45 struct Aligner;
46 struct Stats;
47 
48 struct ComputeThreadSE : public Thread<ComputeThreadSE>
49 {
53  const uint32 _thread_id,
54  const uint32 _device_id,
55  const io::SequenceData& _reference_data,
56  const io::FMIndexData& _driver_data,
57  const std::map<std::string,std::string>& _options,
58  const Params& _params,
59  Stats& _stats);
60 
64 
67  void set_input(InputThreadSE* _input_thread) { input_thread = _input_thread; }
68 
71  void set_output(io::OutputFile* _output_file) { output_file = _output_file; }
72 
73  void run();
74 
75  void do_run();
76 
81  const std::map<std::string,std::string>& options;
89 };
90 
91 struct ComputeThreadPE : public Thread<ComputeThreadPE>
92 {
96  const uint32 _thread_id,
97  const uint32 _device_id,
98  const io::SequenceData& _reference_data,
99  const io::FMIndexData& _driver_data,
100  const std::map<std::string,std::string>& _options,
101  const Params& _params,
102  Stats& _stats);
103 
107 
110  void set_input(InputThreadPE* _input_thread) { input_thread = _input_thread; }
111 
114  void set_output(io::OutputFile* _output_file) { output_file = _output_file; }
115 
116  void run();
117 
118  void do_run();
119 
124  const std::map<std::string,std::string>& options;
132 };
133 
134 } // namespace cuda
135 } // namespace bowtie2
136 } // namespace nvbio