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batched.h
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27 
28 #pragma once
29 
30 #include <nvbio/alignment/alignment.h>
31 
32 namespace nvbio {
33 namespace aln {
34 
37 
48 
51 struct HostThreadScheduler {};
52 
59 template <uint32 BLOCKDIM_T, uint32 MINBLOCKS_T>
60 struct DeviceThreadBlockScheduler
61 {
62  static const uint32 BLOCKDIM = BLOCKDIM_T;
63  static const uint32 MINBLOCKS = MINBLOCKS_T;
64 };
65 
68 typedef DeviceThreadBlockScheduler<128,1> DeviceThreadScheduler;
69 
72 struct DeviceStagedThreadScheduler {};
73 
76 struct DeviceWarpScheduler {};
77 
78 template <typename T,typename Scheduler>
79 struct supports_scheduler { static const bool pred = false; };
80 
81 template <AlignmentType TYPE, typename AlgorithmTag> struct supports_scheduler<EditDistanceAligner<TYPE,AlgorithmTag>, HostThreadScheduler> { static const bool pred = true; };
82 template <AlignmentType TYPE, typename AlgorithmTag> struct supports_scheduler<EditDistanceAligner<TYPE,AlgorithmTag>, DeviceThreadScheduler> { static const bool pred = true; };
83 template <AlignmentType TYPE, typename AlgorithmTag> struct supports_scheduler<EditDistanceAligner<TYPE,AlgorithmTag>, DeviceStagedThreadScheduler> { static const bool pred = true; };
84 template <AlignmentType TYPE, typename AlgorithmTag> struct supports_scheduler<EditDistanceAligner<TYPE,AlgorithmTag>, DeviceWarpScheduler> { static const bool pred = true; };
85 
86 template <AlignmentType TYPE, typename ScoringScheme, typename AlgorithmTag> struct supports_scheduler<SmithWatermanAligner<TYPE,ScoringScheme,AlgorithmTag>, HostThreadScheduler> { static const bool pred = true; };
87 template <AlignmentType TYPE, typename ScoringScheme, typename AlgorithmTag> struct supports_scheduler<SmithWatermanAligner<TYPE,ScoringScheme,AlgorithmTag>, DeviceThreadScheduler> { static const bool pred = true; };
88 template <AlignmentType TYPE, typename ScoringScheme, typename AlgorithmTag> struct supports_scheduler<SmithWatermanAligner<TYPE,ScoringScheme,AlgorithmTag>, DeviceStagedThreadScheduler> { static const bool pred = true; };
89 template <AlignmentType TYPE, typename ScoringScheme, typename AlgorithmTag> struct supports_scheduler<SmithWatermanAligner<TYPE,ScoringScheme,AlgorithmTag>, DeviceWarpScheduler> { static const bool pred = true; };
90 
91 template <AlignmentType TYPE, typename ScoringScheme, typename AlgorithmTag> struct supports_scheduler<GotohAligner<TYPE,ScoringScheme,AlgorithmTag>, HostThreadScheduler> { static const bool pred = true; };
92 template <AlignmentType TYPE, typename ScoringScheme, typename AlgorithmTag> struct supports_scheduler<GotohAligner<TYPE,ScoringScheme,AlgorithmTag>, DeviceThreadScheduler> { static const bool pred = true; };
93 template <AlignmentType TYPE, typename ScoringScheme, typename AlgorithmTag> struct supports_scheduler<GotohAligner<TYPE,ScoringScheme,AlgorithmTag>, DeviceStagedThreadScheduler> { static const bool pred = true; };
94 template <AlignmentType TYPE, typename ScoringScheme, typename AlgorithmTag> struct supports_scheduler<GotohAligner<TYPE,ScoringScheme,AlgorithmTag>, DeviceWarpScheduler> { static const bool pred = true; };
95 
96 template <AlignmentType TYPE, typename ScoringScheme, typename AlgorithmTag> struct supports_scheduler<HammingDistanceAligner<TYPE,ScoringScheme,AlgorithmTag>, HostThreadScheduler> { static const bool pred = true; };
97 template <AlignmentType TYPE, typename ScoringScheme, typename AlgorithmTag> struct supports_scheduler<HammingDistanceAligner<TYPE,ScoringScheme,AlgorithmTag>, DeviceThreadScheduler> { static const bool pred = true; };
98 template <AlignmentType TYPE, typename ScoringScheme, typename AlgorithmTag> struct supports_scheduler<HammingDistanceAligner<TYPE,ScoringScheme,AlgorithmTag>, DeviceStagedThreadScheduler> { static const bool pred = true; };
99 
101 
113 
137 template <
138  typename aligner_type,
139  typename pattern_set_type,
140  typename text_set_type,
141  typename sink_iterator,
142  typename scheduler_type>
143 void batch_alignment_score(
144  const aligner_type aligner,
145  const pattern_set_type patterns,
146  const text_set_type texts,
147  sink_iterator sinks,
148  const scheduler_type scheduler,
149  const uint32 max_pattern_length = 1000,
150  const uint32 max_text_length = 1000);
151 
177 template <
178  typename aligner_type,
179  typename pattern_set_type,
180  typename qualities_set_type,
181  typename text_set_type,
182  typename sink_iterator,
183  typename scheduler_type>
184 void batch_alignment_score(
185  const aligner_type aligner,
186  const pattern_set_type patterns,
187  const qualities_set_type quals,
188  const text_set_type texts,
189  sink_iterator sinks,
190  const scheduler_type scheduler,
191  const uint32 max_pattern_length = 1000,
192  const uint32 max_text_length = 1000);
193 
217 template <
218  uint32 BAND_LEN,
219  typename aligner_type,
220  typename pattern_set_type,
221  typename text_set_type,
222  typename sink_iterator,
223  typename scheduler_type>
224 void batch_banded_alignment_score(
225  const aligner_type aligner,
226  const pattern_set_type patterns,
227  const text_set_type texts,
228  sink_iterator sinks,
229  const scheduler_type scheduler,
230  const uint32 max_pattern_length,
231  const uint32 max_text_length);
232 
310 template <
311  typename stream_type,
312  typename algorithm_type = DeviceThreadScheduler>
313 struct BatchedAlignmentScore
314 {
315  typedef typename stream_type::aligner_type aligner_type;
316  typedef typename checkpoint_storage_type<aligner_type>::type cell_type;
317 
320  static uint64 min_temp_storage(const uint32 max_pattern_len, const uint32 max_text_len, const uint32 stream_size);
321 
324  static uint64 max_temp_storage(const uint32 max_pattern_len, const uint32 max_text_len, const uint32 stream_size);
325 
328  void enact(stream_type stream, uint64 temp_size = 0u, uint8* temp = NULL);
329 };
330 
333 template <
334  uint32 BAND_LEN,
335  typename stream_type,
336  typename algorithm_type = DeviceThreadScheduler>
337 struct BatchedBandedAlignmentScore
338 {
339  typedef typename stream_type::aligner_type aligner_type;
340  typedef typename checkpoint_storage_type<aligner_type>::type cell_type;
341 
344  static uint64 min_temp_storage(const uint32 max_pattern_len, const uint32 max_text_len, const uint32 stream_size);
345 
348  static uint64 max_temp_storage(const uint32 max_pattern_len, const uint32 max_text_len, const uint32 stream_size);
349 
352  void enact(stream_type stream, uint64 temp_size = 0u, uint8* temp = NULL);
353 };
354 
432 template <
433  uint32 CHECKPOINTS,
434  typename stream_type,
435  typename algorithm_type = DeviceThreadScheduler>
436 struct BatchedAlignmentTraceback
437 {
440  static uint64 min_temp_storage(const uint32 max_pattern_len, const uint32 max_text_len, const uint32 stream_size);
441 
444  static uint64 max_temp_storage(const uint32 max_pattern_len, const uint32 max_text_len, const uint32 stream_size);
445 
448  void enact(stream_type stream, uint64 temp_size = 0u, uint8* temp = NULL);
449 };
450 
459 template <
460  uint32 BAND_LEN,
461  uint32 CHECKPOINTS,
462  typename stream_type,
463  typename algorithm_type = DeviceThreadScheduler>
464 struct BatchedBandedAlignmentTraceback
465 {
468  static uint64 min_temp_storage(const uint32 max_pattern_len, const uint32 max_text_len, const uint32 stream_size);
469 
472  static uint64 max_temp_storage(const uint32 max_pattern_len, const uint32 max_text_len, const uint32 stream_size);
473 
476  void enact(stream_type stream, uint64 temp_size = 0u, uint8* temp = NULL);
477 };
478 
480 
482 
483 } // namespace aln
484 } // namespace nvbio
485 
486 #include <nvbio/alignment/batched_inl.h>
487 #include <nvbio/alignment/batched_banded_inl.h>
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