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traceback.h
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27 
28 #pragma once
29 
32 
33 namespace nvbio {
34 namespace io {
35  struct Alignment;
36  struct BestAlignments;
37 } // namespace io
38 } // namespace nvbio
39 
40 namespace nvbio {
41 namespace bowtie2 {
42 namespace cuda {
43 
44 struct ParamsPOD;
45 
46 template <typename ScoringScheme> struct TracebackPipelineState;
47 template <typename ScoringScheme> struct AllMappingPipelineState;
48 
51 
54 
59  const uint32 aln_idx,
60  const uint32 count,
61  const uint32* idx,
62  io::Alignment* best_data,
63  const uint32 best_stride,
64  const uint32 band_len,
65  const TracebackPipelineState<EditDistanceScoringScheme>& pipeline,
66  const ParamsPOD& params);
67 
72  const uint32 aln_idx,
73  const uint32 count,
74  const uint32* idx,
75  io::Alignment* best_data,
76  const uint32 best_stride,
77  const uint32 band_len,
78  const TracebackPipelineState<SmithWatermanScoringScheme<> >& pipeline,
79  const ParamsPOD& params);
80 
85  const uint32 aln_idx,
86  const uint32 count,
87  const uint32* idx,
88  io::Alignment* best_data,
89  const uint32 best_stride,
90  const TracebackPipelineState<EditDistanceScoringScheme>& pipeline,
91  const ParamsPOD& params);
92 
97  const uint32 aln_idx,
98  const uint32 count,
99  const uint32* idx,
100  io::Alignment* best_data,
101  const uint32 best_stride,
102  const TracebackPipelineState<SmithWatermanScoringScheme<> >& pipeline,
103  const ParamsPOD& params);
104 
109  const uint32 count,
110  const uint32* idx,
111  const uint32 buffer_offset,
112  const uint32 buffer_size,
113  io::Alignment* alignments,
114  const uint32 band_len,
115  const AllMappingPipelineState<EditDistanceScoringScheme>& pipeline,
116  const ParamsPOD& params);
117 
122  const uint32 count,
123  const uint32* idx,
124  const uint32 buffer_offset,
125  const uint32 buffer_size,
126  io::Alignment* alignments,
127  const uint32 band_len,
128  const AllMappingPipelineState<SmithWatermanScoringScheme<> >& pipeline,
129  const ParamsPOD& params);
130 
135  const uint32 aln_idx,
136  const uint32 count,
137  const uint32* idx,
138  io::Alignment* best_data,
139  const uint32 best_stride,
140  const uint32 band_len,
141  const TracebackPipelineState<EditDistanceScoringScheme>& pipeline,
142  const SmithWatermanScoringScheme<> scoring_scheme,
143  const ParamsPOD& params);
144 
149  const uint32 aln_idx,
150  const uint32 count,
151  const uint32* idx,
152  io::Alignment* best_data,
153  const uint32 best_stride,
154  const uint32 band_len,
155  const TracebackPipelineState<SmithWatermanScoringScheme<> >& pipeline,
156  const SmithWatermanScoringScheme<> scoring_scheme,
157  const ParamsPOD& params);
158 
163  const uint32 aln_idx,
164  const uint32 count,
165  const uint32* idx,
166  io::Alignment* best_data,
167  const uint32 best_stride,
168  const uint32 band_len,
169  const TracebackPipelineState<EditDistanceScoringScheme>& pipeline,
170  const SmithWatermanScoringScheme<> scoring_scheme,
171  const ParamsPOD& params);
172 
177  const uint32 aln_idx,
178  const uint32 count,
179  const uint32* idx,
180  io::Alignment* best_data,
181  const uint32 best_stride,
182  const uint32 band_len,
183  const TracebackPipelineState<SmithWatermanScoringScheme<> >& pipeline,
184  const SmithWatermanScoringScheme<> scoring_scheme,
185  const ParamsPOD& params);
186 
191  const uint32 count,
192  const uint32* idx,
193  const uint32 buffer_offset,
194  const uint32 buffer_size,
195  io::Alignment* alignments,
196  const uint32 band_len,
197  const AllMappingPipelineState<EditDistanceScoringScheme>& pipeline,
198  const SmithWatermanScoringScheme<> scoring_scheme,
199  const ParamsPOD& params);
200 
205  const uint32 count,
206  const uint32* idx,
207  const uint32 buffer_offset,
208  const uint32 buffer_size,
209  io::Alignment* alignments,
210  const uint32 band_len,
211  const AllMappingPipelineState<SmithWatermanScoringScheme<> >& pipeline,
212  const SmithWatermanScoringScheme<> scoring_scheme,
213  const ParamsPOD& params);
214 
217 
218 } // namespace cuda
219 } // namespace bowtie2
220 } // namespace nvbio