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select.h
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27 
31 
32 #pragma once
33 
40 #include <nvbio/io/alignments.h>
41 
42 namespace nvbio {
43 namespace bowtie2 {
44 namespace cuda {
45 
46 template <typename ScoringScheme> struct BaseScoringPipelineState;
47 template <typename ScoringScheme> struct BestApproxScoringPipelineState;
48 
51 
73 
76 
80 void select_init(
81  const uint32 count,
82  const char* read_names,
83  const uint32* read_names_idx,
84  const SeedHitDequeArrayDeviceView hits,
85  uint32* trys,
86  uint32* rseeds,
87  const ParamsPOD params);
88 
92 void select_init(BestApproxScoringPipelineState<EditDistanceScoringScheme>& pipeline, const ParamsPOD& params);
93 
97 void select_init(BestApproxScoringPipelineState<SmithWatermanScoringScheme<> >& pipeline, const ParamsPOD& params);
98 
103 {
104  // constructor
105  //
106  // \param trys the per-read vector of extension trys
107  //
108  SelectBestApproxContext(uint32* trys) : m_trys( trys ) {}
109 
110  // stopping function
111  //
112  // \return true iff we can stop the hit selection process
113  //
115  bool stop(const uint32 read_id) const { return m_trys[ read_id ] == 0; }
116 
117 private:
118  uint32* m_trys;
119 };
120 
124 __global__
126  const uint32 begin,
127  const uint32 count,
128  const uint32 n_reads,
129  const SeedHit* hit_data,
130  const uint32* hit_range_scan,
131  uint32* loc_queue,
132  uint32* seed_queue,
133  uint32* read_info);
134 
140 void select(
141  const SelectBestApproxContext context,
142  const BestApproxScoringPipelineState<EditDistanceScoringScheme>& pipeline,
143  const ParamsPOD params);
144 
150 void select(
151  const SelectBestApproxContext context,
152  const BestApproxScoringPipelineState<SmithWatermanScoringScheme<> >& pipeline,
153  const ParamsPOD params);
154 
158 void select_all(
159  const uint64 begin,
160  const uint32 count,
161  const uint32 n_reads,
162  const uint32 n_hit_ranges,
163  const uint64 n_hits,
164  const SeedHitDequeArrayDeviceView hits,
165  const uint32* hit_count_scan,
166  const uint64* hit_range_scan,
167  HitQueuesDeviceView scoring_queues);
168 
171 
172 } // namespace cuda
173 } // namespace bowtie2
174 } // namespace nvbio