-
Notifications
You must be signed in to change notification settings - Fork 73
/
classifier.h
1090 lines (994 loc) · 44 KB
/
classifier.h
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
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
/*
* Copyright 2014, Daehwan Kim <[email protected]>
*
* This file is part of HISAT.
*
* HISAT 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, either version 3 of the License, or
* (at your option) any later version.
*
* HISAT 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 should have received a copy of the GNU General Public License
* along with HISAT. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef CLASSIFIER_H_
#define CLASSIFIER_H_
//#define LI_DEBUG
#include <algorithm>
#include <vector>
#include "hi_aligner.h"
#include "util.h"
template<typename index_t>
struct HitCount {
uint64_t uniqueID;
uint64_t taxID;
uint32_t count;
uint32_t score;
uint32_t scores[2][2]; // scores[rdi][fwi]
double summedHitLen;
double summedHitLens[2][2]; // summedHitLens[rdi][fwi]
uint32_t timeStamp;
EList<pair<uint32_t,uint32_t> > readPositions;
bool leaf;
uint32_t num_leaves;
uint8_t _rank; // there are compilation error w/ g++ v7.2.0 on OSX when naming the member 'rank' instead of '_rank'
EList<uint64_t> path;
void reset() {
uniqueID = taxID = count = score = timeStamp = 0;
scores[0][0] = scores[0][1] = scores[1][0] = scores[1][1] = 0;
summedHitLen = 0.0;
summedHitLens[0][0] = summedHitLens[0][1] = summedHitLens[1][0] = summedHitLens[1][1] = 0.0;
readPositions.clear();
_rank = 0;
path.clear();
leaf = true;
num_leaves = 1;
}
HitCount& operator=(const HitCount& o) {
if(this == &o)
return *this;
uniqueID = o.uniqueID;
taxID = o.taxID;
count = o.count;
score = o.score;
scores[0][0] = o.scores[0][0];
scores[0][1] = o.scores[0][1];
scores[1][0] = o.scores[1][0];
scores[1][1] = o.scores[1][1];
summedHitLen = o.summedHitLen;
summedHitLens[0][0] = o.summedHitLens[0][0];
summedHitLens[0][1] = o.summedHitLens[0][1];
summedHitLens[1][0] = o.summedHitLens[1][0];
summedHitLens[1][1] = o.summedHitLens[1][1];
timeStamp = o.timeStamp;
readPositions = o.readPositions;
leaf = o.leaf;
num_leaves = o.num_leaves;
_rank = o._rank;
path = o.path;
return *this;
}
void finalize(
bool paired,
bool mate1fw,
bool mate2fw) {
if(paired) {
#if 1
score = max(scores[0][0], scores[0][1]) + max(scores[1][0], scores[1][1]);
summedHitLen = max(summedHitLens[0][0], summedHitLens[0][1]) + max(summedHitLens[1][0], summedHitLens[1][1]);
#else
uint32_t score1 = 0, score2 = 0;
double summedHitLen1 = 0.0, summedHitLen2 = 0.0;
if(mate1fw == mate2fw) {
score1 = scores[0][0] + scores[1][0];
score2 = scores[0][1] + scores[1][1];
summedHitLen1 = summedHitLens[0][0] + summedHitLens[1][0];
summedHitLen2 = summedHitLens[0][1] + summedHitLens[1][1];
} else {
score1 = scores[0][0] + scores[1][1];
score2 = scores[0][1] + scores[1][0];
summedHitLen1 = summedHitLens[0][0] + summedHitLens[1][1];
summedHitLen2 = summedHitLens[0][1] + summedHitLens[1][0];
}
if(score1 >= score2) {
score = score1;
summedHitLen = summedHitLen1;
} else {
score = score2;
summedHitLen = summedHitLen2;
}
#endif
} else {
score = max(scores[0][0], scores[0][1]);
summedHitLen = max(summedHitLens[0][0], summedHitLens[0][1]);
}
}
};
/**
* With a hierarchical indexing, SplicedAligner provides several alignment strategies
* , which enable effective alignment of RNA-seq reads
*/
template <typename index_t, typename local_index_t>
class Classifier : public HI_Aligner<index_t, local_index_t> {
public:
/**
* Initialize with index.
*/
Classifier(const Ebwt<index_t>& ebwt,
const EList<string>& refnames,
bool mate1fw,
bool mate2fw,
index_t minHitLen,
bool tree_traverse,
const string& classification_rank,
const EList<uint64_t>& hostGenomes,
const EList<uint64_t>& excluded_taxIDs) :
HI_Aligner<index_t, local_index_t>(
ebwt,
0, // don't make use of splice sites found by earlier reads
true), // no spliced alignment
_refnames(refnames),
_minHitLen(minHitLen),
_mate1fw(mate1fw),
_mate2fw(mate2fw),
_tree_traverse(tree_traverse)
{
_classification_rank = get_tax_rank_id(classification_rank.c_str());
_classification_rank = TaxonomyPathTable::rank_to_pathID(_classification_rank);
const map<uint64_t, TaxonomyNode>& tree = ebwt.tree();
_host_taxIDs.clear();
if(hostGenomes.size() > 0) {
for(map<uint64_t, TaxonomyNode>::const_iterator itr = tree.begin(); itr != tree.end(); itr++) {
uint64_t tmp_taxID = itr->first;
while(true) {
bool found = false;
for(size_t t = 0; t < hostGenomes.size(); t++) {
if(tmp_taxID == hostGenomes[t]) {
_host_taxIDs.insert(itr->first);
found = true;
break;
}
}
if(found) break;
map<uint64_t, TaxonomyNode>::const_iterator itr2 = tree.find(tmp_taxID);
if(itr2 == tree.end()) break;
const TaxonomyNode& node = itr2->second;
if(tmp_taxID == node.parent_tid) break;
tmp_taxID = node.parent_tid;
}
}
}
_excluded_taxIDs.clear();
if(excluded_taxIDs.size() > 0) {
for(map<uint64_t, TaxonomyNode>::const_iterator itr = tree.begin(); itr != tree.end(); itr++) {
uint64_t tmp_taxID = itr->first;
while(true) {
bool found = false;
for(size_t t = 0; t < excluded_taxIDs.size(); t++) {
if(tmp_taxID == excluded_taxIDs[t]) {
_excluded_taxIDs.insert(itr->first);
found = true;
break;
}
}
if(found) break;
map<uint64_t, TaxonomyNode>::const_iterator itr2 = tree.find(tmp_taxID);
if(itr2 == tree.end()) break;
if(tmp_taxID == itr2->second.parent_tid) break;
tmp_taxID = itr2->second.parent_tid;
}
}
}
}
~Classifier() {
}
/**
* Aligns a read or a pair
* This funcion is called per read or pair
*/
virtual
int go(
const Scoring& sc,
const Ebwt<index_t>& ebwtFw,
const Ebwt<index_t>& ebwtBw,
const BitPairReference& ref,
WalkMetrics& wlm,
PerReadMetrics& prm,
HIMetrics& him,
SpeciesMetrics& spm,
RandomSource& rnd,
AlnSinkWrap<index_t>& sink)
{
_hitMap.clear();
const index_t increment = (2 * _minHitLen <= 33) ? 10 : (2 * _minHitLen - 33);
const ReportingParams& rp = sink.reportingParams();
index_t maxGenomeHitSize = rp.khits;
bool isFw = false;
//
uint32_t ts = 0; // time stamp
// for each mate. only called once for unpaired data
for(int rdi = 0; rdi < (this->_paired ? 2 : 1); rdi++) {
assert(this->_rds[rdi] != NULL);
// search for partial hits on the forward and reverse strand (saved in this->_hits[rdi])
searchForwardAndReverse(rdi, ebwtFw, sc, rnd, rp, increment);
// get forward or reverse hits for this read from this->_hits[rdi]
// the strand is chosen based on higher average hit length in either direction
pair<int, int> fwp = getForwardOrReverseHit(rdi);
for(int fwi = fwp.first; fwi < fwp.second; fwi++) {
ReadBWTHit<index_t>& hit = this->_hits[rdi][fwi];
assert(hit.done());
isFw = hit._fw; // TODO: Sync between mates!
// choose candidate partial alignments for further alignment
index_t offsetSize = hit.offsetSize();
this->_genomeHits.clear();
// sort partial hits by size (number of genome positions), ascending, and then length, descending
for(size_t hi = 0; hi < offsetSize; hi++) {
const BWTHit<index_t> partialHit = hit.getPartialHit(hi);
#ifdef LI_DEBUG
cout << partialHit.len() << " " << partialHit.size() << endl;
#endif
if(partialHit.len() >= _minHitLen && partialHit.size() > maxGenomeHitSize) {
maxGenomeHitSize = partialHit.size();
}
}
if(maxGenomeHitSize > (index_t)rp.khits) {
maxGenomeHitSize += rp.khits;
}
hit._partialHits.sort(compareBWTHits());
size_t usedPortion = 0;
size_t genomeHitCnt = 0;
for(size_t hi = 0; hi < offsetSize; hi++, ts++) {
const BWTHit<index_t>& partialHit = hit.getPartialHit(hi);
size_t partialHitLen = partialHit.len();
if(partialHitLen <= _minHitLen) continue;
if(partialHit.size() == 0) continue;
// only keep this partial hit if it is equal to or bigger than minHitLen (default: 22 bp)
// TODO: consider not requiring minHitLen when we have already hits to the same genome
bool considerOnlyIfPreviouslyObserved = partialHitLen < _minHitLen;
// get all coordinates of the hit
EList<Coord>& coords = getCoords(
hit,
hi,
ebwtFw,
ref,
rnd,
maxGenomeHitSize,
wlm,
prm,
him);
if(coords.empty())
continue;
usedPortion += partialHitLen;
assert_gt(coords.size(), 0);
// the maximum number of hits per read is maxGenomeHitSize (change with parameter -k)
size_t nHitsToConsider = coords.size();
if((THitInt)coords.size() > rp.ihits) {
continue;
}
// find the genome id for all coordinates, and count the number of genomes
EList<pair<uint64_t, uint64_t> > coord_ids;
for(index_t k = 0; k < nHitsToConsider; k++, genomeHitCnt++) {
const Coord& coord = coords[k];
assert_lt(coord.ref(), _refnames.size()); // gives a warning - coord.ref() is signed integer. why?
// extract numeric id from refName
const EList<pair<string, uint64_t> >& uid_to_tid = ebwtFw.uid_to_tid();
assert_lt(coord.ref(), uid_to_tid.size());
uint64_t taxID = uid_to_tid[coord.ref()].second;
bool found = false;
for(index_t k2 = 0; k2 < coord_ids.size(); k2++) {
// count the genome if it is not in coord_ids, yet
if(coord_ids[k2].first == (uint64_t)coord.ref()) {
found = true;
break;
}
}
if(found) continue;
// add to coord_ids
coord_ids.expand();
coord_ids.back().first = coord.ref();
coord_ids.back().second = taxID;
}
ASSERT_ONLY(size_t n_genomes = coord_ids.size());
// scoring function: calculate the weight of this partial hit
assert_gt(partialHitLen, 15);
assert_gt(n_genomes, 0);
uint32_t partialHitScore = (uint32_t)((partialHitLen - 15) * (partialHitLen - 15)) ; // / n_genomes;
double weightedHitLen = double(partialHitLen) ; // / double(n_genomes) ;
// go through all coordinates reported for partial hit
for(index_t k = 0; k < coord_ids.size(); ++k) {
uint64_t uniqueID = coord_ids[k].first;
uint64_t taxID = coord_ids[k].second;
if(_excluded_taxIDs.find(taxID) != _excluded_taxIDs.end())
continue ;
// add hit to genus map and get new index in the map
size_t idx = addHitToHitMap(
ebwtFw,
_hitMap,
rdi,
fwi,
uniqueID,
taxID,
ts,
partialHitScore,
weightedHitLen,
considerOnlyIfPreviouslyObserved,
partialHit._bwoff,
partialHit.len());
//if considerOnlyIfPreviouslyObserved and it was not found, genus Idx size is equal to the genus Map size
if(idx >= _hitMap.size()) {
continue;
}
#ifdef FLORIAN_DEBUG
std::cerr << speciesID << ';';
#endif
}
if(genomeHitCnt >= maxGenomeHitSize)
break;
#ifdef FLORIAN_DEBUG
std::cerr << " partialHits-done";
#endif
} // partialHits
} // fwi
#ifdef FLORIAN_DEBUG
std::cerr << " rdi-done" << endl;
#endif
} // rdi
for(size_t i = 0; i < _hitMap.size(); i++) {
_hitMap[i].finalize(this->_paired, this->_mate1fw, this->_mate2fw);
}
// See if some of the assignments corresponde to host taxIDs
int64_t best_score = 0;
bool only_host_taxIDs = false;
for(size_t gi = 0; gi < _hitMap.size(); gi++) {
if(_hitMap[gi].score > best_score) {
best_score = _hitMap[gi].score;
only_host_taxIDs = (_host_taxIDs.find(_hitMap[gi].taxID) != _host_taxIDs.end());
} else if(_hitMap[gi].score == best_score) {
only_host_taxIDs |= (_host_taxIDs.find(_hitMap[gi].taxID) != _host_taxIDs.end());
}
}
// If the number of hits is more than -k,
// traverse up the taxonomy tree to reduce the number
if (!only_host_taxIDs && _hitMap.size() > (size_t)rp.khits) {
// Count the number of the best hits
uint32_t best_score = _hitMap[0].score;
for(size_t i = 1; i < _hitMap.size(); i++) {
if(best_score < _hitMap[i].score) {
best_score = _hitMap[i].score;
}
}
// Remove secondary hits
for(int i = 0; i < (int)_hitMap.size(); i++) {
if(_hitMap[i].score < best_score) {
if(i + 1 < (int)_hitMap.size()) {
_hitMap[i] = _hitMap.back();
}
_hitMap.pop_back();
i--;
}
}
if(!_tree_traverse) {
if(_hitMap.size() > (size_t)rp.khits)
{
reportUnclassified( sink ) ;
return 0;
}
}
uint8_t rank = 0;
while(_hitMap.size() > (size_t)rp.khits) {
_hitTaxCount.clear();
for(size_t i = 0; i < _hitMap.size(); i++) {
while(_hitMap[i]._rank < rank) {
if(_hitMap[i]._rank + 1 >= _hitMap[i].path.size()) {
_hitMap[i]._rank = std::numeric_limits<uint8_t>::max();
break;
}
_hitMap[i]._rank += 1;
_hitMap[i].taxID = _hitMap[i].path[_hitMap[i]._rank];
_hitMap[i].leaf = false;
}
if(_hitMap[i]._rank > rank) continue;
uint64_t parent_taxID = (rank + 1 >= _hitMap[i].path.size() ? 1 : _hitMap[i].path[rank + 1]);
// Traverse up the tree more until we get non-zero taxID.
if(parent_taxID == 0) continue;
size_t j = 0;
for(; j < _hitTaxCount.size(); j++) {
if(_hitTaxCount[j].second == parent_taxID) {
_hitTaxCount[j].first += 1;
break;
}
}
if(j == _hitTaxCount.size()) {
_hitTaxCount.expand();
_hitTaxCount.back().first = 1;
_hitTaxCount.back().second = parent_taxID;
}
}
if(_hitTaxCount.size() <= 0) {
if(rank < _hitMap[0].path.size()) {
rank++;
continue;
} else {
break;
}
}
_hitTaxCount.sort();
size_t j = _hitTaxCount.size();
while(j-- > 0) {
uint64_t parent_taxID = _hitTaxCount[j].second;
int64_t max_score = 0;
for(size_t i = 0; i < _hitMap.size(); i++) {
assert_geq(_hitMap[i]._rank, rank);
if(_hitMap[i]._rank != rank) continue;
uint64_t cur_parent_taxID = (rank + 1 >= _hitMap[i].path.size() ? 1 : _hitMap[i].path[rank + 1]);
if(parent_taxID == cur_parent_taxID) {
_hitMap[i].uniqueID = std::numeric_limits<uint64_t>::max();
_hitMap[i]._rank = rank + 1;
_hitMap[i].taxID = parent_taxID;
_hitMap[i].leaf = false;
}
if(parent_taxID == _hitMap[i].taxID) {
if(_hitMap[i].score > max_score) {
max_score = _hitMap[i].score;
}
}
}
bool first = true;
size_t rep_i = _hitMap.size();
for(size_t i = 0; i < _hitMap.size(); i++) {
if(parent_taxID == _hitMap[i].taxID) {
if(!first) {
assert_lt(rep_i, _hitMap.size());
_hitMap[rep_i].num_leaves += _hitMap[i].num_leaves;
if(i + 1 < _hitMap.size()) {
_hitMap[i] = _hitMap.back();
}
_hitMap.pop_back();
i--;
} else {
first = false;
rep_i = i;
}
}
}
if(_hitMap.size() <= (size_t)rp.khits)
break;
}
++rank;
if(rank > _hitMap[0].path.size())
break;
}
}
if(!only_host_taxIDs && _hitMap.size() > (size_t)rp.khits)
{
reportUnclassified( sink ) ;
return 0;
}
#if 0
// boost up the score if the assignment is unique
if(_hitMap.size() == 1) {
HitCount& hitCount = _hitMap[0];
hitCount.score = (hitCount.summedHitLen - 15) * (hitCount.summedHitLen - 15);
}
#endif
index_t rdlen = this->_rds[0]->length();
int64_t max_score = (rdlen > 15 ? (rdlen - 15) * (rdlen - 15) : 0);
if(this->_paired) {
rdlen = this->_rds[1]->length();
max_score += (rdlen > 15 ? (rdlen - 15) * (rdlen - 15) : 0);
}
bool reported = false ;
for(size_t gi = 0; gi < _hitMap.size(); gi++) {
assert_gt(_hitMap[gi].score, 0);
HitCount<index_t>& hitCount = _hitMap[gi];
if(only_host_taxIDs) {
if(_host_taxIDs.find(_hitMap[gi].taxID) == _host_taxIDs.end())
continue;
}
const EList<pair<string, uint64_t> >& uid_to_tid = ebwtFw.uid_to_tid();
const std::map<uint64_t, TaxonomyNode>& tree = ebwtFw.tree();
uint8_t taxRank = RANK_UNKNOWN;
std::map<uint64_t, TaxonomyNode>::const_iterator itr = tree.find(hitCount.taxID);
if(itr != tree.end()) {
taxRank = itr->second.rank;
}
// report
AlnRes rs;
rs.init(
hitCount.score,
max_score,
hitCount.uniqueID < uid_to_tid.size() ? uid_to_tid[hitCount.uniqueID].first : get_tax_rank_string(taxRank),
hitCount.taxID,
taxRank,
hitCount.summedHitLen,
hitCount.readPositions,
isFw);
sink.report(0, &rs);
reported = true ;
}
if ( reported == false )
reportUnclassified( sink ) ;
return 0;
}
bool getGenomeIdx(
const Ebwt<index_t>& ebwt,
const BitPairReference& ref,
RandomSource& rnd,
index_t top,
index_t bot,
bool fw,
index_t maxelt,
index_t rdoff,
index_t rdlen,
EList<Coord>& coords,
WalkMetrics& met,
PerReadMetrics& prm,
HIMetrics& him,
bool rejectStraddle,
bool& straddled)
{
straddled = false;
assert_gt(bot, top);
index_t nelt = bot - top;
nelt = min<index_t>(nelt, maxelt);
coords.clear();
him.globalgenomecoords += (bot - top);
this->_offs.resize(nelt);
this->_offs.fill(std::numeric_limits<index_t>::max());
this->_sas.init(top, rdlen, EListSlice<index_t, 16>(this->_offs, 0, nelt));
this->_gws.init(ebwt, ref, this->_sas, rnd, met);
for(index_t off = 0; off < nelt; off++) {
WalkResult<index_t> wr;
this->_gws.advanceElement(
off,
ebwt, // forward Bowtie index for walking left
ref, // bitpair-encoded reference
this->_sas, // SA range with offsets
this->_gwstate, // GroupWalk state; scratch space
wr, // put the result here
met, // metrics
prm); // per-read metrics
// Coordinate of the seed hit w/r/t the pasted reference string
coords.expand();
coords.back().init(wr.toff, 0, fw);
}
return true;
}
void reportUnclassified( AlnSinkWrap<index_t>& sink )
{
AlnRes rs ;
EList<pair<uint32_t,uint32_t> > dummy ;
dummy.push_back( make_pair( 0, 0 ) ) ;
rs.init( 0, 0, string( "unclassified" ), 0, 0, 0, dummy, true ) ;
sink.report( 0, &rs ) ;
}
private:
EList<string> _refnames;
EList<HitCount<index_t> > _hitMap;
index_t _minHitLen;
EList<uint16_t> _tempTies;
bool _mate1fw;
bool _mate2fw;
bool _tree_traverse;
uint8_t _classification_rank;
set<uint64_t> _host_taxIDs; // favor these genomes
set<uint64_t> _excluded_taxIDs;
// Temporary variables
ReadBWTHit<index_t> _tempHit;
EList<pair<uint32_t, uint64_t> > _hitTaxCount; // pair of count and taxID
EList<uint64_t> _tempPath;
void searchForwardAndReverse(
index_t rdi,
const Ebwt<index_t>& ebwtFw,
const Scoring& sc,
RandomSource& rnd,
const ReportingParams& rp,
const index_t increment)
{
const Read& rd = *(this->_rds[rdi]);
bool done[2] = {false, false};
#ifdef LI_DEBUG
size_t cur[2] = {0, 0} ;
#endif
index_t rdlen = rd.length();
//const size_t maxDiff = (rdlen / 2 > 2 * _minHitLen) ? rdlen / 2 : (2 * _minHitLen);
size_t sum[2] = {0, 0} ;
// search for partial hits on the forward and reverse strand
while(!done[0] || !done[1]) {
for(index_t fwi = 0; fwi < 2; fwi++) {
if(done[fwi])
continue;
size_t mineFw = 0, mineRc = 0;
bool fw = (fwi == 0);
ReadBWTHit<index_t>& hit = this->_hits[rdi][fwi];
this->partialSearch(
ebwtFw,
rd,
sc,
fw,
0,
mineFw,
mineRc,
hit,
rnd);
BWTHit<index_t>& lastHit = hit.getPartialHit(hit.offsetSize() - 1);
if(hit.done()) {
done[fwi] = true;
#ifdef LI_DEBUG
cur[fwi] = rdlen;
#endif
if(lastHit.len() >= _minHitLen) {
sum[fwi] += lastHit.len();
if(0) //lastHit.len() < 31 && rdlen > 31 && lastHit.size() == 1 )
{
ReadBWTHit<index_t> testHit ;
testHit.init( fw, rdlen ) ;
testHit.setOffset(hit.cur() - 1 - 31 + 1);
this->partialSearch(ebwtFw,
rd,
sc,
fw,
0,
mineFw,
mineRc,
testHit,
rnd);
index_t tmpLen = testHit.getPartialHit( testHit.offsetSize() - 1 ).len();
#ifdef LI_DEBUG
cout << "(adjust: " << tmpLen << ")";
#endif
if(tmpLen >= 31) {
lastHit._len = tmpLen;
}
}
}
continue;
}
#ifdef LI_DEBUG
cur[fwi] = hit.cur();
cout << fwi << ":" << lastHit.len() << " " << cur[fwi] << " ";
#endif
if(lastHit.len() >= _minHitLen)
sum[fwi] += lastHit.len();
if(lastHit.len() > increment) {
if(lastHit.len() < _minHitLen) {
// daehwan - for debugging purposes
#if 1
hit.setOffset(hit.cur() + 1);
#else
hit.setOffset(hit.cur() - increment);
#endif
} else {
hit.setOffset(hit.cur() + 1);
if(0) //lastHit.len() < 31 && hit.cur() >= 31 && lastHit.size() == 1 )
{
ReadBWTHit<index_t> testHit;
testHit.init(fw, rdlen);
testHit.setOffset(hit.cur() - 1 - 31); // why not hit.cur() - 1 - 31 + 1? because we "+1" before the if!
this->partialSearch(ebwtFw,
rd,
sc,
fw,
0,
mineFw,
mineRc,
testHit,
rnd);
index_t tmpLen = testHit.getPartialHit(testHit.offsetSize() - 1 ).len();
#ifdef LI_DEBUG
cout << "(adjust: " << tmpLen << ")";
#endif
if(tmpLen >= 31) {
lastHit._len = tmpLen;
}
}
}
}
if(hit.cur() + _minHitLen >= rdlen) {
hit.done(true);
done[fwi] = true;
continue;
}
if(lastHit.len() <= 3) {
// This happens most likely due to the Ns in the read
--fwi ; // Repeat this strand again.
}
}
#ifdef LI_DEBUG
cout << endl;
#endif
// No early termination
#if 0
if(sum[0] > sum[1] + (rdlen - cur[1] + 1)) {
this->_hits[rdi][1].done(true);
done[1] = true;
} else if(sum[1] > sum[0] + (rdlen - cur[0] + 1)) {
this->_hits[rdi][0].done(true);
done[0] = true;
}
#endif
}
// Extend partial hits
if(sum[0] >= _minHitLen && sum[1] >= _minHitLen) {
ReadBWTHit<index_t>& hits = this->_hits[rdi][0];
ReadBWTHit<index_t>& rchits = this->_hits[rdi][1];
for(size_t i = 0; i < hits.offsetSize(); i++) {
BWTHit<index_t>& hit = hits.getPartialHit(i);
index_t len = hit.len();
//if(len < _minHitLen) continue;
index_t l = hit._bwoff;
index_t r = hit._bwoff + len;
for(size_t j = 0; j < rchits.offsetSize(); j++) {
BWTHit<index_t>& rchit = rchits.getPartialHit(j);
index_t rclen = rchit.len();
if(len < _minHitLen && rclen < _minHitLen) continue;
index_t rc_l = rdlen - rchit._bwoff - rchit._len;
index_t rc_r = rc_l + rclen;
if(r <= rc_l) continue;
if(rc_r <= l) continue;
if(l == rc_l && r == rc_r) continue;
if(l < rc_l && r > rc_r) continue;
if(l > rc_l && r < rc_r) continue;
if(l > rc_l) {
_tempHit.init(true /* fw */, rdlen);
_tempHit.setOffset(rc_l);
size_t mineFw = 0, mineRc = 0;
this->partialSearch(ebwtFw,
rd,
sc,
true, // fw
0,
mineFw,
mineRc,
_tempHit,
rnd);
BWTHit<index_t>& tmphit = _tempHit.getPartialHit(0);
if(tmphit.len() == len + l - rc_l) {
hit = tmphit;
}
}
if(r > rc_r) {
_tempHit.init(false /* fw */, rdlen);
_tempHit.setOffset(rdlen - r);
size_t mineFw = 0, mineRc = 0;
this->partialSearch(ebwtFw,
rd,
sc,
false, // fw
0,
mineFw,
mineRc,
_tempHit,
rnd);
BWTHit<index_t>& tmphit = _tempHit.getPartialHit(0);
if(tmphit.len() == rclen + r - rc_r) {
rchit = tmphit;
}
}
}
}
// Remove partial hits that are mapped more than user-specified number
for(size_t i = 0; i < hits.offsetSize(); i++) {
BWTHit<index_t>& hit = hits.getPartialHit(i);
index_t len = hit.len();
index_t l = hit._bwoff;
index_t r = hit._bwoff + len;
for(size_t j = 0; j < rchits.offsetSize(); j++) {
BWTHit<index_t>& rchit = rchits.getPartialHit(j);
index_t rclen = rchit.len();
index_t rc_l = rdlen - rchit._bwoff - rchit._len;
index_t rc_r = rc_l + rclen;
if(rc_l < l) break;
if(len != rclen) continue;
if(l == rc_l &&
r == rc_r &&
hit.size() + rchit.size() > rp.ihits) {
hit.reset();
rchit.reset();
break;
}
}
}
}
// Trim partial hits
for(int fwi = 0; fwi < 2; fwi++) {
ReadBWTHit<index_t>& hits = this->_hits[rdi][fwi];
if(hits.offsetSize() < 2) continue;
for(size_t i = 0; i < hits.offsetSize() - 1; i++) {
BWTHit<index_t>& hit = hits.getPartialHit(i);
for(size_t j = i + 1; j < hits.offsetSize(); j++) {
BWTHit<index_t>& hit2 = hits.getPartialHit(j);
if(hit._bwoff >= hit2._bwoff) {
hit._len = 0;
break;
}
if(hit._bwoff + hit._len <= hit2._bwoff) break;
if(hit._len >= hit2._len) {
index_t hit2_end = hit2._bwoff + hit2._len;
hit2._bwoff = hit._bwoff + hit._len;
hit2._len = hit2_end - hit2._bwoff;
} else {
hit._len = hit2._bwoff - hit._bwoff;
}
}
}
}
}
pair<int, int> getForwardOrReverseHit(index_t rdi) {
index_t avgHitLength[2] = {0, 0};
index_t hitSize[2] = {0, 0} ;
index_t maxHitLength[2] = {0, 0} ;
for(index_t fwi = 0; fwi < 2; fwi++) {
ReadBWTHit<index_t>& hit = this->_hits[rdi][fwi];
index_t numHits = 0;
index_t totalHitLength = 0;
#ifdef LI_DEBUG
cout << fwi << ": ";
#endif
for(size_t i = 0; i < hit.offsetSize(); i++) {
index_t len = hit.getPartialHit(i).len();
#ifdef LI_DEBUG
cout << len << " ";
#endif
if(len < _minHitLen) continue;
totalHitLength += (len - 15) * (len - 15);
hitSize[fwi] += hit.getPartialHit(i).size();
if(len > maxHitLength[fwi])
maxHitLength[fwi] = len;
numHits++;
}
#ifdef LI_DEBUG
cout << endl;
#endif
if(numHits > 0) {
avgHitLength[fwi] = totalHitLength ; /// numHits;
}
}
// choose read direction with a higher average hit length
//cout<<"strand choosing: "<<avgHitLength[0]<<" "<<avgHitLength[1]<<endl ;
index_t fwi;//= (avgHitLength[0] > avgHitLength[1])? 0 : 1;
if(avgHitLength[0] != avgHitLength[1])
fwi = (avgHitLength[0] > avgHitLength[1]) ? 0 : 1;
else if(maxHitLength[0] != maxHitLength[1])
fwi = (maxHitLength[0] > maxHitLength[1])? 0 : 1;
else
return pair<int, int>(0, 2);
return pair<int, int>((int)fwi, (int)fwi + 1);
}
EList<Coord>& getCoords(
ReadBWTHit<index_t>& hit,
size_t hi,
const Ebwt<index_t>& ebwtFw,
const BitPairReference& ref,
RandomSource& rnd,
const index_t maxGenomeHitSize,
WalkMetrics& wlm,
PerReadMetrics& prm,
HIMetrics& him)
{
BWTHit<index_t>& partialHit = hit.getPartialHit(hi);
assert(!partialHit.hasGenomeCoords());
bool straddled = false;
this->getGenomeIdx(
ebwtFw, // FB: Why is it called ...FW here?
ref,
rnd,
partialHit._top,
partialHit._bot,
hit._fw == 0, // FIXME: fwi and hit._fw are defined differently
maxGenomeHitSize - this->_genomeHits.size(),
hit._len - partialHit._bwoff - partialHit._len,
partialHit._len,
partialHit._coords,
wlm, // why is it called wlm here?
prm,
him,
false, // reject straddled
straddled);
#ifdef FLORIAN_DEBUG
std::cerr << partialHit.len() << ':';
#endif
// get all coordinates of the hit
return partialHit._coords;
}
// append a hit to genus map or update entry
size_t addHitToHitMap(
const Ebwt<index_t>& ebwt,
EList<HitCount<index_t> >& hitMap,
int rdi,
int fwi,
uint64_t uniqueID,
uint64_t taxID,
size_t hi,
uint32_t partialHitScore,
double weightedHitLen,
bool considerOnlyIfPreviouslyObserved,
size_t offset,
size_t length)
{
size_t idx = 0;
#ifdef LI_DEBUG
cout << "Add " << taxID << " " << partialHitScore << " " << weightedHitLen << endl;
#endif
const TaxonomyPathTable& pathTable = ebwt.paths();