1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
|
/*
Ray -- Parallel genome assemblies for parallel DNA sequencing
Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#ifndef _MessageProcessor_h
#define _MessageProcessor_h
#include <code/SeedExtender/OpenAssemblerChooser.h>
#include <code/SeedExtender/SeedExtender.h>
#include <code/SequencesLoader/ArrayOfReads.h>
#include <code/SequencesLoader/SequencesLoader.h>
#include <code/SequencesIndexer/ReadAnnotation.h>
#include <code/SequencesIndexer/SequencesIndexer.h>
#include <code/KmerAcademyBuilder/BloomFilter.h>
#include <code/Library/Library.h>
#include <code/SeedingData/SeedingData.h>
#include <code/FusionData/FusionData.h>
#include <code/VerticesExtractor/VerticesExtractor.h>
#include <code/VerticesExtractor/Vertex.h>
#include <code/VerticesExtractor/GridTable.h>
#include <code/Mock/Parameters.h>
#include <code/Scaffolder/Scaffolder.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/memory/MyAllocator.h>
#include <RayPlatform/structures/SplayTree.h>
#include <RayPlatform/structures/StaticVector.h>
#include <RayPlatform/communication/Message.h>
#include <RayPlatform/communication/BufferedData.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <RayPlatform/communication/MessageRouter.h>
#include <RayPlatform/scheduling/SwitchMan.h>
#include <RayPlatform/plugins/CorePlugin.h>
#include <RayPlatform/core/ComputeCore.h>
#include <vector>
using namespace std;
__DeclarePlugin(MessageProcessor);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_CONTIG_INFO);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_SCAFFOLDING_LINKS);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_GET_READ_MARKERS);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_GET_READ_MATE);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_READS);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_SET_WORD_SIZE);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_VERTEX_READS);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_VERTEX_INFO);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_VERTEX_READS_FROM_LIST);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_START_INDEXING_SEQUENCES);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_SEQUENCES_READY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_VERTICES_DATA);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_PURGE_NULL_EDGES);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_VERTICES_DISTRIBUTED);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_OUT_EDGES_DATA_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_OUT_EDGES_DATA);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_START_VERTICES_DISTRIBUTION);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_IN_EDGES_DATA_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_IN_EDGES_DATA); /**/
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION_QUESTION);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION_ANSWER);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_COVERAGE_DATA);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_COVERAGE_END);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_SEND_COVERAGE_VALUES);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_READY_TO_SEED);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_START_SEEDING);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_GET_COVERAGE_AND_MARK);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_EDGES);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_EDGES_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_SEEDING_IS_OVER);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_SEED_LENGTHS);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_SEND_SEED_LENGTHS);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_IS_DONE_SENDING_SEED_LENGTHS);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ACTIVATE_RELAY_CHECKER);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_MASTER_IS_DONE_ATTACHING_READS);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_MASTER_IS_DONE_ATTACHING_READS_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_INGOING_EDGES);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_INGOING_EDGES_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_EXTENSION_IS_DONE);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_EXTENSION);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_EXTENSION_DATA_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_EXTENSION_DATA);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ATTACH_SEQUENCE);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ATTACH_SEQUENCE_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_READ_VERTEX_AT_POSITION);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_READ_VERTEX_AT_POSITION_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_READ_LENGTH);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_READ_LENGTH_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_SAVE_WAVE_PROGRESSION_WITH_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_SAVE_WAVE_PROGRESSION);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_SAVE_WAVE_PROGRESSION_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASSEMBLE_WAVES);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASSEMBLE_WAVES_DONE);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_START_FUSION);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_FUSION_DONE);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_GET_PATH_LENGTH);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_GET_PATH_LENGTH_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATHS);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATHS_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATHS_REPLY_END);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATH);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATH_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_HAS_PAIRED_READ);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_HAS_PAIRED_READ_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_GET_PAIRED_READ);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_GET_PAIRED_READ_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_CLEAR_DIRECTIONS);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_CLEAR_DIRECTIONS_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_FINISH_FUSIONS);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_FINISH_FUSIONS_FINISHED);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_DISTRIBUTE_FUSIONS);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_DISTRIBUTE_FUSIONS_FINISHED_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_DISTRIBUTE_FUSIONS_FINISHED);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_EXTENSION_START);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ELIMINATE_PATH);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_GET_PATH_VERTEX);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_GET_PATH_VERTEX_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_WRITE_AMOS);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_WRITE_AMOS_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_AUTOMATIC_DISTANCE_DETECTION);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_AUTOMATIC_DISTANCE_DETECTION_IS_DONE);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_LIBRARY_DISTANCE_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_LIBRARY_DISTANCE);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_LIBRARY_DISTANCES);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_ASK_LIBRARY_DISTANCES_FINISHED);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_UPDATE_LIBRARY_INFORMATION);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_KMER_ACADEMY_DISTRIBUTED);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_SEND_COVERAGE_VALUES_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_READ_SEQUENCE);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_READ_SEQUENCE_REPLY);
__DeclareMessageTagAdapter(MessageProcessor,RAY_MPI_TAG_I_FINISHED_SCAFFOLDING);
__DeclareMessageTagAdapter(MessageProcessor, RAY_MESSAGE_TAG_PUSH_SEEDS);
__DeclareMessageTagAdapter(MessageProcessor, RAY_MESSAGE_TAG_PUSH_SEEDS_REPLY);
/**
* MessageProcessor receives all the messages of a MPI rank
* Message objects may also be checked using the Message inbox (m_inbox)
*
* Sometimes, a message will generate a reply (_REPLY)
*
* \author Sébastien Boisvert
*/
class MessageProcessor : public CorePlugin {
__AddAdapter(MessageProcessor,RAY_MPI_TAG_CONTIG_INFO);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_SCAFFOLDING_LINKS);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_GET_READ_MARKERS);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_GET_READ_MATE);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_READS);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_SET_WORD_SIZE);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_VERTEX_READS);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_VERTEX_INFO);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_VERTEX_READS_FROM_LIST);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_START_INDEXING_SEQUENCES);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_SEQUENCES_READY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_VERTICES_DATA);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_PURGE_NULL_EDGES);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_VERTICES_DISTRIBUTED);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_OUT_EDGES_DATA_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_OUT_EDGES_DATA);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_START_VERTICES_DISTRIBUTION);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_IN_EDGES_DATA_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_IN_EDGES_DATA); /**/
__AddAdapter(MessageProcessor,RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION_QUESTION);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION_ANSWER);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_COVERAGE_DATA);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_COVERAGE_END);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_SEND_COVERAGE_VALUES);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_READY_TO_SEED);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_START_SEEDING);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_GET_COVERAGE_AND_MARK);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_EDGES);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_EDGES_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_SEEDING_IS_OVER);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_SEED_LENGTHS);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_SEND_SEED_LENGTHS);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_IS_DONE_SENDING_SEED_LENGTHS);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ACTIVATE_RELAY_CHECKER);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_MASTER_IS_DONE_ATTACHING_READS);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_MASTER_IS_DONE_ATTACHING_READS_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_INGOING_EDGES);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_VERTEX_INGOING_EDGES_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_EXTENSION_IS_DONE);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_EXTENSION);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_EXTENSION_DATA_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_EXTENSION_DATA);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ATTACH_SEQUENCE);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ATTACH_SEQUENCE_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_READ_VERTEX_AT_POSITION);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_READ_VERTEX_AT_POSITION_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_READ_LENGTH);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_READ_LENGTH_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_SAVE_WAVE_PROGRESSION_WITH_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_SAVE_WAVE_PROGRESSION);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_SAVE_WAVE_PROGRESSION_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASSEMBLE_WAVES);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASSEMBLE_WAVES_DONE);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_START_FUSION);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_FUSION_DONE);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_GET_PATH_LENGTH);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_GET_PATH_LENGTH_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATHS);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATHS_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATHS_REPLY_END);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATH);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_VERTEX_PATH_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_HAS_PAIRED_READ);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_HAS_PAIRED_READ_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_GET_PAIRED_READ);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_GET_PAIRED_READ_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_CLEAR_DIRECTIONS);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_CLEAR_DIRECTIONS_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_FINISH_FUSIONS);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_FINISH_FUSIONS_FINISHED);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_DISTRIBUTE_FUSIONS);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_DISTRIBUTE_FUSIONS_FINISHED_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_DISTRIBUTE_FUSIONS_FINISHED);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_EXTENSION_START);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ELIMINATE_PATH);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_GET_PATH_VERTEX);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_GET_PATH_VERTEX_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_WRITE_AMOS);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_WRITE_AMOS_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_AUTOMATIC_DISTANCE_DETECTION);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_AUTOMATIC_DISTANCE_DETECTION_IS_DONE);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_LIBRARY_DISTANCE_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_LIBRARY_DISTANCE);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_LIBRARY_DISTANCES);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_ASK_LIBRARY_DISTANCES_FINISHED);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_UPDATE_LIBRARY_INFORMATION);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_KMER_ACADEMY_DISTRIBUTED);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_SEND_COVERAGE_VALUES_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_READ_SEQUENCE);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_REQUEST_READ_SEQUENCE_REPLY);
__AddAdapter(MessageProcessor,RAY_MPI_TAG_I_FINISHED_SCAFFOLDING);
__AddAdapter(MessageProcessor, RAY_MESSAGE_TAG_PUSH_SEEDS);
__AddAdapter(MessageProcessor, RAY_MESSAGE_TAG_PUSH_SEEDS_REPLY);
uint64_t m_bloomBits;
MessageTag RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION;
MessageTag RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION_ANSWER;
MessageTag RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION_QUESTION;
MessageTag RAY_MPI_TAG_PURGE_NULL_EDGES;
MessageTag RAY_MPI_TAG_READY_TO_SEED;
MessageTag RAY_MPI_TAG_REQUEST_READ_SEQUENCE;
MessageTag RAY_MPI_TAG_REQUEST_READ_SEQUENCE_REPLY;
MessageTag RAY_MPI_TAG_REQUEST_SEED_LENGTHS;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE_REPLY;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_EDGES;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_EDGES_REPLY;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_INGOING_EDGES;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_INGOING_EDGES_REPLY;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES_REPLY;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_READS;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_READS_REPLY;
MessageTag RAY_MPI_TAG_SAVE_WAVE_PROGRESSION;
MessageTag RAY_MPI_TAG_SAVE_WAVE_PROGRESSION_REPLY;
MessageTag RAY_MPI_TAG_SAVE_WAVE_PROGRESSION_WITH_REPLY;
MessageTag RAY_MPI_TAG_SCAFFOLDING_LINKS;
MessageTag RAY_MPI_TAG_SCAFFOLDING_LINKS_REPLY;
MessageTag RAY_MPI_TAG_SEEDING_IS_OVER;
MessageTag RAY_MPI_TAG_SEND_COVERAGE_VALUES;
MessageTag RAY_MPI_TAG_SEND_COVERAGE_VALUES_REPLY;
MessageTag RAY_MPI_TAG_SEND_SEED_LENGTHS;
MessageTag RAY_MPI_TAG_SEND_SEED_LENGTHS_REPLY;
MessageTag RAY_MPI_TAG_SEQUENCES_READY;
MessageTag RAY_MPI_TAG_SET_WORD_SIZE;
MessageTag RAY_MPI_TAG_START_FUSION;
MessageTag RAY_MPI_TAG_START_INDEXING_SEQUENCES;
MessageTag RAY_MPI_TAG_START_SEEDING;
MessageTag RAY_MPI_TAG_START_VERTICES_DISTRIBUTION;
MessageTag RAY_MPI_TAG_TEST_NETWORK_MESSAGE;
MessageTag RAY_MPI_TAG_TEST_NETWORK_MESSAGE_REPLY;
MessageTag RAY_MPI_TAG_UPDATE_LIBRARY_INFORMATION;
MessageTag RAY_MPI_TAG_UPDATE_LIBRARY_INFORMATION_REPLY;
MessageTag RAY_MPI_TAG_VERTEX_INFO;
MessageTag RAY_MPI_TAG_VERTEX_INFO_REPLY;
MessageTag RAY_MPI_TAG_VERTEX_READS;
MessageTag RAY_MPI_TAG_VERTEX_READS_FROM_LIST;
MessageTag RAY_MPI_TAG_VERTEX_READS_FROM_LIST_REPLY;
MessageTag RAY_MPI_TAG_VERTEX_READS_REPLY;
MessageTag RAY_MPI_TAG_VERTICES_DATA;
MessageTag RAY_MPI_TAG_VERTICES_DATA_REPLY;
MessageTag RAY_MPI_TAG_VERTICES_DISTRIBUTED;
MessageTag RAY_MPI_TAG_WRITE_AMOS;
MessageTag RAY_MPI_TAG_WRITE_AMOS_REPLY;
MessageTag RAY_MPI_TAG_CONTIG_INFO;
MessageTag RAY_MPI_TAG_CONTIG_INFO_REPLY;
MessageTag RAY_MPI_TAG_COVERAGE_DATA;
MessageTag RAY_MPI_TAG_COVERAGE_DATA_REPLY;
MessageTag RAY_MPI_TAG_COVERAGE_END;
MessageTag RAY_MPI_TAG_DISTRIBUTE_FUSIONS;
MessageTag RAY_MPI_TAG_DISTRIBUTE_FUSIONS_FINISHED;
MessageTag RAY_MPI_TAG_DISTRIBUTE_FUSIONS_FINISHED_REPLY;
MessageTag RAY_MPI_TAG_DISTRIBUTE_FUSIONS_FINISHED_REPLY_REPLY;
MessageTag RAY_MPI_TAG_ELIMINATE_PATH;
MessageTag RAY_MPI_TAG_EXTENSION_DATA;
MessageTag RAY_MPI_TAG_EXTENSION_DATA_REPLY;
MessageTag RAY_MPI_TAG_EXTENSION_IS_DONE;
MessageTag RAY_MPI_TAG_EXTENSION_START;
MessageTag RAY_MPI_TAG_FINISH_FUSIONS;
MessageTag RAY_MPI_TAG_FINISH_FUSIONS_FINISHED;
MessageTag RAY_MPI_TAG_FUSION_DONE;
MessageTag RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION;
MessageTag RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION_REPLY;
MessageTag RAY_MPI_TAG_GET_COVERAGE_AND_MARK;
MessageTag RAY_MPI_TAG_GET_COVERAGE_AND_MARK_REPLY;
MessageTag RAY_MPI_TAG_GET_PAIRED_READ;
MessageTag RAY_MPI_TAG_GET_PAIRED_READ_REPLY;
MessageTag RAY_MPI_TAG_GET_PATH_LENGTH;
MessageTag RAY_MPI_TAG_GET_PATH_LENGTH_REPLY;
MessageTag RAY_MPI_TAG_GET_PATH_VERTEX;
MessageTag RAY_MPI_TAG_GET_PATH_VERTEX_REPLY;
MessageTag RAY_MPI_TAG_GET_READ_MARKERS;
MessageTag RAY_MPI_TAG_GET_READ_MARKERS_REPLY;
MessageTag RAY_MPI_TAG_GET_READ_MATE;
MessageTag RAY_MPI_TAG_GET_READ_MATE_REPLY;
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT;
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT_REPLY;
MessageTag RAY_MPI_TAG_HAS_PAIRED_READ;
MessageTag RAY_MPI_TAG_HAS_PAIRED_READ_REPLY;
MessageTag RAY_MPI_TAG_I_FINISHED_SCAFFOLDING;
MessageTag RAY_MPI_TAG_IN_EDGES_DATA;
MessageTag RAY_MPI_TAG_IN_EDGES_DATA_REPLY;
MessageTag RAY_MPI_TAG_IS_DONE_SENDING_SEED_LENGTHS;
MessageTag RAY_MPI_TAG_KMER_ACADEMY_DATA;
MessageTag RAY_MPI_TAG_KMER_ACADEMY_DATA_REPLY;
MessageTag RAY_MPI_TAG_KMER_ACADEMY_DISTRIBUTED;
MessageTag RAY_MPI_TAG_LIBRARY_DISTANCE;
MessageTag RAY_MPI_TAG_LIBRARY_DISTANCE_REPLY;
MessageTag RAY_MPI_TAG_MASTER_IS_DONE_ATTACHING_READS;
MessageTag RAY_MPI_TAG_MASTER_IS_DONE_ATTACHING_READS_REPLY;
MessageTag RAY_MPI_TAG_OUT_EDGES_DATA;
MessageTag RAY_MPI_TAG_OUT_EDGES_DATA_REPLY;
MessageTag RAY_MPI_TAG_ACTIVATE_RELAY_CHECKER;
MessageTag RAY_MPI_TAG_ACTIVATE_RELAY_CHECKER_REPLY;
MessageTag RAY_MPI_TAG_ASK_EXTENSION;
MessageTag RAY_MPI_TAG_ASK_LIBRARY_DISTANCES;
MessageTag RAY_MPI_TAG_ASK_LIBRARY_DISTANCES_FINISHED;
MessageTag RAY_MPI_TAG_ASK_READ_LENGTH;
MessageTag RAY_MPI_TAG_ASK_READ_LENGTH_REPLY;
MessageTag RAY_MPI_TAG_ASK_READ_VERTEX_AT_POSITION;
MessageTag RAY_MPI_TAG_ASK_READ_VERTEX_AT_POSITION_REPLY;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATH_REPLY;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_REPLY;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_REPLY_END;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE;
MessageTag RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE_REPLY;
MessageTag RAY_MPI_TAG_ASSEMBLE_WAVES;
MessageTag RAY_MPI_TAG_ASSEMBLE_WAVES_DONE;
MessageTag RAY_MPI_TAG_ATTACH_SEQUENCE;
MessageTag RAY_MPI_TAG_ATTACH_SEQUENCE_REPLY;
MessageTag RAY_MPI_TAG_AUTOMATIC_DISTANCE_DETECTION;
MessageTag RAY_MPI_TAG_AUTOMATIC_DISTANCE_DETECTION_IS_DONE;
MessageTag RAY_MPI_TAG_CLEAR_DIRECTIONS;
MessageTag RAY_MPI_TAG_CLEAR_DIRECTIONS_REPLY;
MessageTag RAY_MESSAGE_TAG_PUSH_SEEDS;
MessageTag RAY_MESSAGE_TAG_PUSH_SEEDS_REPLY;
MasterMode RAY_MASTER_MODE_ASK_DISTANCES;
MasterMode RAY_MASTER_MODE_DO_NOTHING;
MasterMode RAY_MASTER_MODE_PREPARE_SEEDING;
MasterMode RAY_MASTER_MODE_PURGE_NULL_EDGES;
MasterMode RAY_MASTER_MODE_START_UPDATING_DISTANCES;
MasterMode RAY_MASTER_MODE_TRIGGER_DETECTION;
MasterMode RAY_MASTER_MODE_TRIGGER_FIRST_FUSIONS;
MasterMode RAY_MASTER_MODE_TRIGGER_FUSIONS;
MasterMode RAY_MASTER_MODE_TRIGGER_SEEDING;
MasterMode RAY_MASTER_MODE_WRITE_SCAFFOLDS;
MasterMode RAY_MASTER_MODE_REGISTER_SEEDS;
SlaveMode RAY_SLAVE_MODE_PURGE_NULL_EDGES;
SlaveMode RAY_SLAVE_MODE_AMOS;
SlaveMode RAY_SLAVE_MODE_ASSEMBLE_WAVES;
SlaveMode RAY_SLAVE_MODE_AUTOMATIC_DISTANCE_DETECTION;
SlaveMode RAY_SLAVE_MODE_ADD_VERTICES;
SlaveMode RAY_SLAVE_MODE_DISTRIBUTE_FUSIONS;
SlaveMode RAY_SLAVE_MODE_EXTENSION;
SlaveMode RAY_SLAVE_MODE_FINISH_FUSIONS;
SlaveMode RAY_SLAVE_MODE_FUSION;
SlaveMode RAY_SLAVE_MODE_INDEX_SEQUENCES;
SlaveMode RAY_SLAVE_MODE_LOAD_SEQUENCES;
SlaveMode RAY_SLAVE_MODE_SEND_DISTRIBUTION;
SlaveMode RAY_SLAVE_MODE_SEND_EXTENSION_DATA;
SlaveMode RAY_SLAVE_MODE_SEND_LIBRARY_DISTANCES;
SlaveMode RAY_SLAVE_MODE_SEND_SEED_LENGTHS;
SlaveMode RAY_SLAVE_MODE_START_SEEDING;
MessageRouter*m_router;
int m_kmerAcademyFinishedRanks;
BloomFilter m_bloomFilter;
VirtualCommunicator*m_virtualCommunicator;
Scaffolder*m_scaffolder;
int m_count;
uint64_t m_lastSize;
SequencesLoader*m_sequencesLoader;
uint64_t m_sentinelValue;
SeedingData*m_seedingData;
/* switch man for synchronization
*/
SwitchMan*m_switchMan;
// data for processing
bool*m_ready;
int m_consumed;
time_t m_last;
Library*m_library;
bool*m_isFinalFusion;
int*m_master_mode;
ExtensionData*m_ed;
int*m_numberOfRanksDoneDetectingDistances;
int*m_numberOfRanksDoneSendingDistances;
Parameters*m_parameters;
GridTable*m_subgraph;
RingAllocator*m_outboxAllocator;
int m_rank;
int*m_numberOfMachinesDoneSendingEdges;
FusionData*m_fusionData;
ArrayOfReads*m_myReads;
int m_size;
SequencesIndexer*m_si;
RingAllocator*m_inboxAllocator;
MyAllocator*m_persistentAllocator;
vector<PathHandle>*m_identifiers;
bool*m_mode_sendDistribution;
bool*m_alive;
int*m_mode;
vector<vector<uint64_t> >*m_allPaths;
int*m_last_value;
int*m_ranksDoneAttachingReads;
int*m_DISTRIBUTE_n;
int*m_numberOfRanksDoneSeeding;
int*m_CLEAR_n;
int*m_readyToSeed;
int*m_FINISH_n;
bool*m_nextReductionOccured;
MyAllocator*m_directionsAllocator;
int*m_mode_send_coverage_iterator;
map<CoverageDepth,LargeCount>*m_coverageDistribution;
int*m_sequence_ready_machines;
int*m_numberOfMachinesReadyForEdgesDistribution;
int*m_numberOfMachinesReadyToSendDistribution;
bool*m_mode_send_outgoing_edges;
int*m_mode_send_vertices_sequence_id;
bool*m_mode_send_vertices;
int*m_numberOfMachinesDoneSendingVertices;
VerticesExtractor*m_verticesExtractor;
int*m_numberOfMachinesDoneSendingCoverage;
StaticVector*m_outbox;
StaticVector*m_inbox;
map<int,int>*m_allIdentifiers;
OpenAssemblerChooser*m_oa;
int*m_numberOfRanksWithCoverageData;
SeedExtender*seedExtender;
public:
void constructor(
MessageRouter*router,
SeedingData*seedingData,
Library*m_library,
bool*m_ready,
VerticesExtractor*m_verticesExtractor,
SequencesLoader*m_sequencesLoader,
ExtensionData*ed,
int*m_numberOfRanksDoneDetectingDistances,
int*m_numberOfRanksDoneSendingDistances,
Parameters*parameters,
GridTable*m_subgraph,
RingAllocator*m_outboxAllocator,
int rank,
int*m_numberOfMachinesDoneSendingEdges,
FusionData*m_fusionData,
ArrayOfReads*m_myReads,
int size,
RingAllocator*m_inboxAllocator,
MyAllocator*m_persistentAllocator,
vector<PathHandle>*m_identifiers,
bool*m_mode_sendDistribution,
bool*m_alive,
int*m_mode,
vector<vector<uint64_t> >*m_allPaths,
int*m_last_value,
int*m_ranksDoneAttachingReads,
int*m_DISTRIBUTE_n,
int*m_numberOfRanksDoneSeeding,
int*m_CLEAR_n,
int*m_readyToSeed,
int*m_FINISH_n,
bool*m_nextReductionOccured,
int*m_mode_send_coverage_iterator,
map<CoverageDepth,LargeCount>*m_coverageDistribution,
int*m_sequence_ready_machines,
int*m_numberOfMachinesReadyForEdgesDistribution,
int*m_numberOfMachinesReadyToSendDistribution,
bool*m_mode_send_outgoing_edges,
int*m_mode_send_vertices_sequence_id,
bool*m_mode_send_vertices,
int*m_numberOfMachinesDoneSendingVertices,
int*m_numberOfMachinesDoneSendingCoverage,
StaticVector*m_outbox,
StaticVector*m_inbox,
OpenAssemblerChooser*m_oa,
int*m_numberOfRanksWithCoverageData,
SeedExtender*seedExtender,int*m_master_mode,bool*m_isFinalFusion,
SequencesIndexer*m_si
);
void processMessage(Message*message);
MessageProcessor();
void flushBuffers();
void setScaffolder(Scaffolder*a);
void setVirtualCommunicator(VirtualCommunicator*a);
void setSwitchMan(SwitchMan*a);
// list of declarations
void call_RAY_MPI_TAG_CONTIG_INFO(Message*message);
void call_RAY_MPI_TAG_SCAFFOLDING_LINKS(Message*message);
void call_RAY_MPI_TAG_GET_READ_MARKERS(Message*message);
void call_RAY_MPI_TAG_GET_READ_MATE(Message*message);
void call_RAY_MPI_TAG_REQUEST_VERTEX_READS(Message*message);
void call_RAY_MPI_TAG_SET_WORD_SIZE(Message*message);
void call_RAY_MPI_TAG_VERTEX_READS(Message*message);
void call_RAY_MPI_TAG_VERTEX_INFO(Message*message);
void call_RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT(Message*message);
void call_RAY_MPI_TAG_VERTEX_READS_FROM_LIST(Message*message);
void call_RAY_MPI_TAG_START_INDEXING_SEQUENCES(Message*message);
void call_RAY_MPI_TAG_SEQUENCES_READY(Message*message);
void call_RAY_MPI_TAG_VERTICES_DATA(Message*message);
void call_RAY_MPI_TAG_PURGE_NULL_EDGES(Message*message);
void call_RAY_MPI_TAG_VERTICES_DISTRIBUTED(Message*message);
void call_RAY_MPI_TAG_OUT_EDGES_DATA_REPLY(Message*message);
void call_RAY_MPI_TAG_OUT_EDGES_DATA(Message*message);
void call_RAY_MPI_TAG_START_VERTICES_DISTRIBUTION(Message*message);
void call_RAY_MPI_TAG_IN_EDGES_DATA_REPLY(Message*message);
void call_RAY_MPI_TAG_IN_EDGES_DATA(Message*message);
void call_RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION_QUESTION(Message*message);
void call_RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION_ANSWER(Message*message);
void call_RAY_MPI_TAG_PREPARE_COVERAGE_DISTRIBUTION(Message*message);
void call_RAY_MPI_TAG_COVERAGE_DATA(Message*message);
void call_RAY_MPI_TAG_COVERAGE_END(Message*message);
void call_RAY_MPI_TAG_SEND_COVERAGE_VALUES(Message*message);
void call_RAY_MPI_TAG_READY_TO_SEED(Message*message);
void call_RAY_MPI_TAG_START_SEEDING(Message*message);
void call_RAY_MPI_TAG_GET_COVERAGE_AND_MARK(Message*message);
void call_RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE(Message*message);
void call_RAY_MPI_TAG_REQUEST_VERTEX_COVERAGE_REPLY(Message*message);
void call_RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES(Message*message);
void call_RAY_MPI_TAG_REQUEST_VERTEX_EDGES(Message*message);
void call_RAY_MPI_TAG_REQUEST_VERTEX_EDGES_REPLY(Message*message);
void call_RAY_MPI_TAG_REQUEST_VERTEX_OUTGOING_EDGES_REPLY(Message*message);
void call_RAY_MPI_TAG_SEEDING_IS_OVER(Message*message);
void call_RAY_MPI_TAG_REQUEST_SEED_LENGTHS(Message*message);
void call_RAY_MPI_TAG_SEND_SEED_LENGTHS(Message*message);
void call_RAY_MPI_TAG_IS_DONE_SENDING_SEED_LENGTHS(Message*message);
void call_RAY_MPI_TAG_ACTIVATE_RELAY_CHECKER(Message*message);
void call_RAY_MPI_TAG_MASTER_IS_DONE_ATTACHING_READS(Message*message);
void call_RAY_MPI_TAG_MASTER_IS_DONE_ATTACHING_READS_REPLY(Message*message);
void call_RAY_MPI_TAG_REQUEST_VERTEX_INGOING_EDGES(Message*message);
void call_RAY_MPI_TAG_REQUEST_VERTEX_INGOING_EDGES_REPLY(Message*message);
void call_RAY_MPI_TAG_EXTENSION_IS_DONE(Message*message);
void call_RAY_MPI_TAG_ASK_EXTENSION(Message*message);
void call_RAY_MPI_TAG_EXTENSION_DATA_REPLY(Message*message);
void call_RAY_MPI_TAG_EXTENSION_DATA(Message*message);
void call_RAY_MPI_TAG_ATTACH_SEQUENCE(Message*message);
void call_RAY_MPI_TAG_ATTACH_SEQUENCE_REPLY(Message*message);
void call_RAY_MPI_TAG_ASK_READ_VERTEX_AT_POSITION(Message*message);
void call_RAY_MPI_TAG_ASK_READ_VERTEX_AT_POSITION_REPLY(Message*message);
void call_RAY_MPI_TAG_ASK_READ_LENGTH(Message*message);
void call_RAY_MPI_TAG_ASK_READ_LENGTH_REPLY(Message*message);
void call_RAY_MPI_TAG_SAVE_WAVE_PROGRESSION_WITH_REPLY(Message*message);
void call_RAY_MPI_TAG_SAVE_WAVE_PROGRESSION(Message*message);
void call_RAY_MPI_TAG_SAVE_WAVE_PROGRESSION_REPLY(Message*message);
void call_RAY_MPI_TAG_ASSEMBLE_WAVES(Message*message);
void call_RAY_MPI_TAG_ASSEMBLE_WAVES_DONE(Message*message);
void call_RAY_MPI_TAG_START_FUSION(Message*message);
void call_RAY_MPI_TAG_FUSION_DONE(Message*message);
void call_RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE(Message*message);
void call_RAY_MPI_TAG_ASK_VERTEX_PATHS_SIZE_REPLY(Message*message);
void call_RAY_MPI_TAG_GET_PATH_LENGTH(Message*message);
void call_RAY_MPI_TAG_GET_COVERAGE_AND_DIRECTION(Message*message);
void call_RAY_MPI_TAG_GET_PATH_LENGTH_REPLY(Message*message);
void call_RAY_MPI_TAG_ASK_VERTEX_PATHS(Message*message);
void call_RAY_MPI_TAG_ASK_VERTEX_PATHS_REPLY(Message*message);
void call_RAY_MPI_TAG_ASK_VERTEX_PATHS_REPLY_END(Message*message);
void call_RAY_MPI_TAG_ASK_VERTEX_PATH(Message*message);
void call_RAY_MPI_TAG_ASK_VERTEX_PATH_REPLY(Message*message);
void call_RAY_MPI_TAG_HAS_PAIRED_READ(Message*message);
void call_RAY_MPI_TAG_HAS_PAIRED_READ_REPLY(Message*message);
void call_RAY_MPI_TAG_GET_PAIRED_READ(Message*message);
void call_RAY_MPI_TAG_GET_PAIRED_READ_REPLY(Message*message);
void call_RAY_MPI_TAG_CLEAR_DIRECTIONS(Message*message);
void call_RAY_MPI_TAG_CLEAR_DIRECTIONS_REPLY(Message*message);
void call_RAY_MPI_TAG_FINISH_FUSIONS(Message*message);
void call_RAY_MPI_TAG_FINISH_FUSIONS_FINISHED(Message*message);
void call_RAY_MPI_TAG_DISTRIBUTE_FUSIONS(Message*message);
void call_RAY_MPI_TAG_DISTRIBUTE_FUSIONS_FINISHED_REPLY(Message*message);
void call_RAY_MPI_TAG_DISTRIBUTE_FUSIONS_FINISHED(Message*message);
void call_RAY_MPI_TAG_EXTENSION_START(Message*message);
void call_RAY_MPI_TAG_ELIMINATE_PATH(Message*message);
void call_RAY_MPI_TAG_GET_PATH_VERTEX(Message*message);
void call_RAY_MPI_TAG_GET_PATH_VERTEX_REPLY(Message*message);
void call_RAY_MPI_TAG_WRITE_AMOS(Message*message);
void call_RAY_MPI_TAG_WRITE_AMOS_REPLY(Message*message);
void call_RAY_MPI_TAG_AUTOMATIC_DISTANCE_DETECTION(Message*message);
void call_RAY_MPI_TAG_AUTOMATIC_DISTANCE_DETECTION_IS_DONE(Message*message);
void call_RAY_MPI_TAG_LIBRARY_DISTANCE_REPLY(Message*message);
void call_RAY_MPI_TAG_LIBRARY_DISTANCE(Message*message);
void call_RAY_MPI_TAG_ASK_LIBRARY_DISTANCES(Message*message);
void call_RAY_MPI_TAG_ASK_LIBRARY_DISTANCES_FINISHED(Message*message);
void call_RAY_MPI_TAG_UPDATE_LIBRARY_INFORMATION(Message*message);
void call_RAY_MPI_TAG_KMER_ACADEMY_DATA(Message*message);
void call_RAY_MPI_TAG_KMER_ACADEMY_DISTRIBUTED(Message*message);
void call_RAY_MPI_TAG_SEND_COVERAGE_VALUES_REPLY(Message*message);
void call_RAY_MPI_TAG_REQUEST_READ_SEQUENCE(Message*message);
void call_RAY_MPI_TAG_REQUEST_READ_SEQUENCE_REPLY(Message*message);
void call_RAY_MPI_TAG_I_FINISHED_SCAFFOLDING(Message*message);
void call_RAY_MESSAGE_TAG_PUSH_SEEDS(Message*message);
void call_RAY_MESSAGE_TAG_PUSH_SEEDS_REPLY(Message*message);
void registerPlugin(ComputeCore*core);
void resolveSymbols(ComputeCore*core);
};
#endif
|
