forked from DaehwanKimLab/hisat
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathspliced_aligner.h
1285 lines (1255 loc) · 71.5 KB
/
spliced_aligner.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 SPLICED_ALIGNER_H_
#define SPLICED_ALIGNER_H_
#include "hi_aligner.h"
/**
* 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 SplicedAligner : public HI_Aligner<index_t, local_index_t> {
public:
/**
* Initialize with index.
*/
SplicedAligner(
const Ebwt<index_t>& ebwt,
size_t minIntronLen,
size_t maxIntronLen,
bool secondary = false,
bool local = false,
uint64_t threads_rids_mindist = 0,
bool no_spliced_alignment = false) :
HI_Aligner<index_t, local_index_t>(ebwt,
minIntronLen,
maxIntronLen,
secondary,
local,
threads_rids_mindist,
no_spliced_alignment)
{
}
~SplicedAligner() {
}
/**
* Given a partial alignment of a read, try to further extend
* the alignment bidirectionally using a combination of
* local search, extension, and global search
*/
virtual
void hybridSearch(
const Scoring& sc,
const Ebwt<index_t>& ebwtFw,
const Ebwt<index_t>& ebwtBw,
const BitPairReference& ref,
SwAligner& swa,
SpliceSiteDB& ssdb,
index_t rdi,
bool fw,
WalkMetrics& wlm,
PerReadMetrics& prm,
SwMetrics& swm,
HIMetrics& him,
RandomSource& rnd,
AlnSinkWrap<index_t>& sink);
/**
* Given a partial alignment of a read, try to further extend
* the alignment bidirectionally using a combination of
* local search, extension, and global search
*/
virtual
int64_t hybridSearch_recur(
const Scoring& sc,
const Ebwt<index_t>& ebwtFw,
const Ebwt<index_t>& ebwtBw,
const BitPairReference& ref,
SwAligner& swa,
SpliceSiteDB& ssdb,
index_t rdi,
const GenomeHit<index_t>& hit,
index_t hitoff,
index_t hitlen,
WalkMetrics& wlm,
PerReadMetrics& prm,
SwMetrics& swm,
HIMetrics& him,
RandomSource& rnd,
AlnSinkWrap<index_t>& sink,
index_t dep = 0);
};
/**
* Given a partial alignment of a read, try to further extend
* the alignment bidirectionally using a combination of
* local search, extension, and global search
*/
template <typename index_t, typename local_index_t>
void SplicedAligner<index_t, local_index_t>::hybridSearch(
const Scoring& sc,
const Ebwt<index_t>& ebwtFw,
const Ebwt<index_t>& ebwtBw,
const BitPairReference& ref,
SwAligner& swa,
SpliceSiteDB& ssdb,
index_t rdi,
bool fw,
WalkMetrics& wlm,
PerReadMetrics& prm,
SwMetrics& swm,
HIMetrics& him,
RandomSource& rnd,
AlnSinkWrap<index_t>& sink)
{
assert_lt(rdi, 2);
assert(this->_rds[rdi] != NULL);
him.localatts++;
// before further alignment using local search, extend the partial alignments directly
// by comparing with the corresponding genomic sequences
// this extension is performed without any mismatches allowed
for(index_t hi = 0; hi < this->_genomeHits.size(); hi++) {
GenomeHit<index_t>& genomeHit = this->_genomeHits[hi];
index_t leftext = (index_t)OFF_MASK, rightext = (index_t)OFF_MASK;
genomeHit.extend(
*(this->_rds[rdi]),
ref,
ssdb,
swa,
swm,
prm,
sc,
this->_minsc[rdi],
rnd,
this->_minK_local,
this->_minIntronLen,
this->_maxIntronLen,
leftext,
rightext);
}
// for the candidate alignments, examine the longest (best) one first
this->_genomeHits_done.resize(this->_genomeHits.size());
this->_genomeHits_done.fill(false);
for(size_t hi = 0; hi < this->_genomeHits.size(); hi++) {
index_t hj = 0;
for(; hj < this->_genomeHits.size(); hj++) {
if(!this->_genomeHits_done[hj]) break;
}
if(hj >= this->_genomeHits.size()) break;
for(index_t hk = hj + 1; hk < this->_genomeHits.size(); hk++) {
if(this->_genomeHits_done[hk]) continue;
GenomeHit<index_t>& genomeHit_j = this->_genomeHits[hj];
GenomeHit<index_t>& genomeHit_k = this->_genomeHits[hk];
if(genomeHit_k.hitcount() > genomeHit_j.hitcount() ||
(genomeHit_k.hitcount() == genomeHit_j.hitcount() && genomeHit_k.len() > genomeHit_j.len())) {
hj = hk;
}
}
// given a candidate partial alignment, extend it bidirectionally
him.anchoratts++;
GenomeHit<index_t>& genomeHit = this->_genomeHits[hj];
hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
genomeHit,
genomeHit.rdoff(),
genomeHit.len(),
wlm,
prm,
swm,
him,
rnd,
sink);
this->_genomeHits_done[hj] = true;
}
}
/**
* Given a partial alignment of a read, try to further extend
* the alignment bidirectionally using a combination of
* local search, extension, and global search
*/
template <typename index_t, typename local_index_t>
int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(
const Scoring& sc,
const Ebwt<index_t>& ebwtFw,
const Ebwt<index_t>& ebwtBw,
const BitPairReference& ref,
SwAligner& swa,
SpliceSiteDB& ssdb,
index_t rdi,
const GenomeHit<index_t>& hit,
index_t hitoff,
index_t hitlen,
WalkMetrics& wlm,
PerReadMetrics& prm,
SwMetrics& swm,
HIMetrics& him,
RandomSource& rnd,
AlnSinkWrap<index_t>& sink,
index_t dep)
{
int64_t maxsc = numeric_limits<int64_t>::min();
him.localsearchrecur++;
assert_lt(rdi, 2);
assert(this->_rds[rdi] != NULL);
const Read& rd = *(this->_rds[rdi]);
index_t rdlen = rd.length();
if(hit.score() < this->_minsc[rdi]) return maxsc;
// if it's already examined, just return
if(hitoff == hit.rdoff() - hit.trim5() && hitlen == hit.len() + hit.trim5() + hit.trim3()) {
if(this->isSearched(hit, rdi)) return maxsc;
this->addSearched(hit, rdi);
}
// for effective use of memory allocation and deallocation
if(this->_coords.size() <= dep) {
this->_coords.expand();
assert_leq(this->_local_genomeHits.size(), dep);
this->_local_genomeHits.expand();
assert_leq(this->_spliceSites.size(), dep);
this->_spliceSites.expand();
}
EList<Coord>& coords = this->_coords[dep];
EList<GenomeHit<index_t> >& local_genomeHits = this->_local_genomeHits[dep];
EList<SpliceSite>& spliceSites = this->_spliceSites[dep];
// daehwan - for debugging purposes
#if 0
cout << rd.name << "\t"
<< (hit.fw() ? "+" : "-") << "\t"
<< hitoff << "\t"
<< hitoff + hitlen << "\t"
<< "( " << hit.rdoff() << "\t"
<< hit.rdoff() + hit.len() << " )" << "\t"
<< hit.refoff() << "\t"
<< hit.getRightOff() << "\t"
<< hit.score() << "\t"
<< "dep: " << dep << "\t";
Edit::print(cout, hit.edits());
cout << endl;
#endif
assert_leq(hitoff + hitlen, rdlen);
// if this is a full alignment, report it
if(hitoff == 0 && hitlen == rdlen) {
if(!this->redundant(sink, rdi, hit)) {
bool another_spliced = false;
if(!ssdb.empty()) {
int64_t best_score = hit.score();
local_genomeHits.clear();
this->_anchors_added.clear();
local_genomeHits.expand();
local_genomeHits.back() = hit;
this->_anchors_added.push_back(0);
index_t fragoff = 0, fraglen = 0, left = 0, right = 0;
hit.getLeft(fragoff, fraglen, left);
const index_t minMatchLen = this->_minK;
index_t min_left_anchor = rdlen, min_right_anchor = rdlen;
// make use of a list of known or novel splice sites to further align the read
if(fraglen >= minMatchLen &&
left >= minMatchLen &&
hit.trim5() == 0 &&
!this->_no_spliced_alignment) {
spliceSites.clear();
ssdb.getLeftSpliceSites(hit.ref(), left + minMatchLen, minMatchLen, spliceSites);
for(size_t si = 0; si < spliceSites.size(); si++) {
const SpliceSite& ss = spliceSites[si];
if(!ss._fromfile && ss._readid + this->_thread_rids_mindist > rd.rdid) continue;
if(left + fraglen - 1 < ss.right()) continue;
index_t frag2off = ss.left() - (ss.right() - left);
if(frag2off + 1 < hitoff) continue;
GenomeHit<index_t> tempHit;
tempHit.init(hit.fw(),
0,
hitoff,
0, // trim5
0, // trim3
hit.ref(),
frag2off + 1,
this->_sharedVars);
if(!tempHit.compatibleWith(hit, this->_minIntronLen, this->_maxIntronLen, this->_no_spliced_alignment)) continue;
int64_t minsc = max<int64_t>(this->_minsc[rdi], best_score);
bool combined = tempHit.combineWith(hit, rd, ref, ssdb, swa, swm, sc, minsc, rnd, this->_minK_local, this->_minIntronLen, this->_maxIntronLen, 1, 1, &ss);
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
index_t leftAnchorLen = 0, nedits = 0;
tempHit.getLeftAnchor(leftAnchorLen, nedits);
if(combined &&
tempHit.score() >= minsc &&
nedits <= leftAnchorLen / 4) { // prevent (short) anchors from having many mismatches
if(!this->redundant(sink, rdi, tempHit)) {
another_spliced = true;
if(tempHit.score() > best_score)
best_score = tempHit.score();
local_genomeHits.expand();
local_genomeHits.back() = tempHit;
this->_anchors_added.push_back(1);
index_t temp_fragoff = 0, temp_fraglen = 0, temp_left = 0;
tempHit.getLeft(temp_fragoff, temp_fraglen, temp_left);
if(temp_fraglen < min_left_anchor)
min_left_anchor = temp_fraglen;
}
}
}
}
size_t num_local_genomeHits = local_genomeHits.size();
for(size_t i = 0; i < num_local_genomeHits; i++) {
local_genomeHits[i].getRight(fragoff, fraglen, right);
if(local_genomeHits[i].score() < best_score) continue;
// make use of a list of known or novel splice sites to further align the read
if(fraglen >= minMatchLen &&
local_genomeHits[i].trim3() == 0 &&
!this->_no_spliced_alignment) {
spliceSites.clear();
assert_gt(fraglen, 0);
ssdb.getRightSpliceSites(local_genomeHits[i].ref(), right + fraglen - minMatchLen, minMatchLen, spliceSites);
for(size_t si = 0; si < spliceSites.size(); si++) {
const GenomeHit<index_t>& canHit = local_genomeHits[i];
const SpliceSite& ss = spliceSites[si];
if(!ss._fromfile && ss._readid + this->_thread_rids_mindist > rd.rdid) continue;
if(right > ss.left()) continue;
index_t frag2off = ss.right() - ss.left() + right + fraglen - 1;
GenomeHit<index_t> tempHit;
tempHit.init(canHit.fw(),
fragoff + fraglen,
rdlen - fragoff - fraglen,
0, // trim5
0, // trim3
canHit.ref(),
frag2off,
this->_sharedVars);
if(!canHit.compatibleWith(tempHit, this->_minIntronLen, this->_maxIntronLen, this->_no_spliced_alignment)) continue;
GenomeHit<index_t> combinedHit = canHit;
int64_t minsc = max<int64_t>(this->_minsc[rdi], best_score);
bool combined = combinedHit.combineWith(tempHit, rd, ref, ssdb, swa, swm, sc, minsc, rnd, this->_minK_local, this->_minIntronLen, this->_maxIntronLen, 1, 1, &ss);
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
index_t rightAnchorLen = 0, nedits = 0;
combinedHit.getRightAnchor(rightAnchorLen, nedits);
if(combined &&
combinedHit.score() >= minsc &&
nedits <= rightAnchorLen / 4) { // prevent (short) anchors from having many mismatches
if(!this->redundant(sink, rdi, combinedHit)) {
another_spliced = true;
if(combinedHit.score() > best_score)
best_score = tempHit.score();
local_genomeHits.expand();
local_genomeHits.back() = combinedHit;
this->_anchors_added.push_back(this->_anchors_added[i] + 1);
index_t temp_fragoff = 0, temp_fraglen = 0, temp_right = 0;
combinedHit.getLeft(temp_fragoff, temp_fraglen, temp_right);
if(temp_fraglen < min_right_anchor)
min_right_anchor = temp_fraglen;
}
}
}
}
}
assert_eq(local_genomeHits.size(), this->_anchors_added.size());
for(size_t i = 0; i < local_genomeHits.size(); i++) {
const GenomeHit<index_t>& canHit = local_genomeHits[i];
if(!this->_secondary && canHit.score() < best_score) continue;
// if(min(min_left_anchor, min_right_anchor) <= this->_minK_local) {
if(this->_anchors_added[i] < this->_anchors_added.back()) continue;
//}
if(!this->redundant(sink, rdi, canHit)) {
this->reportHit(sc, ebwtFw, ref, ssdb, sink, rdi, canHit);
maxsc = max<int64_t>(maxsc, canHit.score());
}
}
}
else {
this->reportHit(sc, ebwtFw, ref, ssdb, sink, rdi, hit);
maxsc = max<int64_t>(maxsc, hit.score());
}
return maxsc;
}
} else if(hitoff > 0 && (hitoff + hitlen == rdlen || hitoff + hitoff < rdlen - hitlen)) {
if(!ssdb.empty()) {
// extend the partial alignment in the left direction
index_t fragoff = 0, fraglen = 0, left = 0;
hit.getLeft(fragoff, fraglen, left);
const index_t minMatchLen = this->_minK_local;
// make use of a list of known or novel splice sites to further align the read
if(fraglen >= minMatchLen && left >= minMatchLen && !this->_no_spliced_alignment) {
spliceSites.clear();
ssdb.getLeftSpliceSites(hit.ref(), left + minMatchLen, minMatchLen + min<index_t>(minMatchLen, fragoff), spliceSites);
for(size_t si = 0; si < spliceSites.size(); si++) {
const SpliceSite& ss = spliceSites[si];
if(!ss._fromfile && ss._readid + this->_thread_rids_mindist > rd.rdid) continue;
if(left + fraglen - 1 < ss.right()) continue;
index_t frag2off = ss.left() - (ss.right() - left);
if(frag2off + 1 < hitoff) continue;
GenomeHit<index_t> tempHit;
tempHit.init(hit.fw(),
0, // rdoff
fragoff, // len
0, // trim5
0, // trim3
hit.ref(),
frag2off + 1 - fragoff,
this->_sharedVars);
if(!tempHit.compatibleWith(hit, this->_minIntronLen, this->_maxIntronLen, this->_no_spliced_alignment)) continue;
int64_t minsc = this->_minsc[rdi];
bool combined = tempHit.combineWith(hit, rd, ref, ssdb, swa, swm, sc, minsc, rnd, this->_minK_local, this->_minIntronLen, this->_maxIntronLen, 1, 1, &ss);
if(!this->_secondary) {
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
}
index_t leftAnchorLen = 0, nedits = 0;
tempHit.getLeftAnchor(leftAnchorLen, nedits);
if(combined &&
tempHit.score() >= minsc &&
nedits <= leftAnchorLen / 4) { // prevent (short) anchors from having many mismatches
assert_eq(tempHit.trim5(), 0);
assert_leq(tempHit.rdoff() + tempHit.len() + tempHit.trim3(), rdlen);
int64_t tmp_maxsc = hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
tempHit,
tempHit.rdoff(),
tempHit.len() + tempHit.trim3(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
maxsc = max<int64_t>(maxsc, tmp_maxsc);
}
}
}
}
bool use_localindex = true;
if(hitoff == hit.rdoff() && hitoff <= this->_minK) {
index_t leftext = (index_t)OFF_MASK, rightext = (index_t)0;
GenomeHit<index_t> tempHit = hit;
tempHit.extend(rd, ref, ssdb, swa, swm, prm, sc, this->_minsc[rdi], rnd, this->_minK_local, this->_minIntronLen, this->_maxIntronLen, leftext, rightext, 1);
if(tempHit.rdoff() == 0) {
use_localindex = false;
}
}
// choose a local index based on the genomic location of the partial alignment
const HierEbwt<index_t, local_index_t>* hierEbwtFw = (const HierEbwt<index_t, local_index_t>*)(&ebwtFw);
const LocalEbwt<local_index_t, index_t>* localEbwtFw = hierEbwtFw->getLocalEbwt(hit.ref(), hit.refoff());
assert_leq(localEbwtFw->_localOffset, hit.refoff());
bool success = false, first = true;
index_t count = 0;
// consider at most two local indexes
index_t max_count = 2;
int64_t prev_score = hit.score();
local_genomeHits.clear();
while(!success && count++ < max_count && use_localindex) {
if(him.localindexatts >= this->max_localindexatts) break;
if(first) {
first = false;
} else {
localEbwtFw = hierEbwtFw->prevLocalEbwt(localEbwtFw);
if(localEbwtFw == NULL || localEbwtFw->empty()) break;
}
// local index search
index_t extlen = 0;
local_index_t top = (local_index_t)OFF_MASK, bot = (local_index_t)OFF_MASK;
index_t extoff = hitoff - 1;
if(extoff > 0) extoff -= 1;
if(extoff < minAnchorLen) {
extoff = minAnchorLen;
}
index_t nelt = (index_t)OFF_MASK;
index_t max_nelt = std::max<index_t>(5, extlen);
bool no_extension = false;
bool uniqueStop;
index_t minUniqueLen = this->_minK_local;
for(; extoff < rdlen; extoff++) {
extlen = 0;
uniqueStop = true;
him.localindexatts++;
nelt = this->localEbwtSearch(
localEbwtFw, // BWT index
NULL, // BWT index
rd, // read to align
sc, // scoring scheme
hit.fw(),
false, // searchfw,
extoff,
extlen,
top,
bot,
rnd,
uniqueStop,
minUniqueLen);
if(extoff + 1 - extlen >= hitoff) {
no_extension = true;
break;
}
if(nelt <= max_nelt) break;
}
assert_leq(top, bot);
assert_eq(nelt, (index_t)(bot - top));
assert_leq(extlen, extoff + 1);
if(nelt > 0 &&
nelt <= max_nelt &&
extlen >= minAnchorLen &&
!no_extension) {
assert_leq(nelt, max_nelt);
coords.clear();
bool straddled = false;
// get genomic locations for this local search
this->getGenomeCoords_local(
*localEbwtFw,
ref,
rnd,
top,
bot,
hit.fw(),
extoff + 1 - extlen,
extlen,
coords,
wlm,
prm,
him,
true, // reject straddled?
straddled);
assert_leq(coords.size(), nelt);
coords.sort();
for(int ri = coords.size() - 1; ri >= 0; ri--) {
const Coord& coord = coords[ri];
GenomeHit<index_t> tempHit;
tempHit.init(coord.orient(),
extoff + 1 - extlen,
extlen,
0, // trim5
0, // trim3
coord.ref(),
coord.off(),
this->_sharedVars);
// check if the partial alignment is compatible with the new alignment using the local index
if(!tempHit.compatibleWith(hit, this->_minIntronLen, this->_maxIntronLen, this->_no_spliced_alignment)) {
if(count == 1) continue;
else break;
}
if(uniqueStop) {
assert_eq(coords.size(), 1);
index_t leftext = (index_t)OFF_MASK, rightext = (index_t)0;
tempHit.extend(rd, ref, ssdb, swa, swm, prm, sc, this->_minsc[rdi], rnd, this->_minK_local, this->_minIntronLen, this->_maxIntronLen, leftext, rightext);
}
// combine the partial alignment and the new alignment
int64_t minsc = this->_minsc[rdi];
bool combined = tempHit.combineWith(hit, rd, ref, ssdb, swa, swm, sc, minsc, rnd, this->_minK_local, this->_minIntronLen, this->_maxIntronLen);
if(!this->_secondary) {
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
}
if(combined && tempHit.score() >= minsc) {
assert_eq(tempHit.trim5(), 0);
assert_leq(tempHit.rdoff() + tempHit.len() + tempHit.trim3(), rdlen);
if(tempHit.score() >= prev_score - sc.mmpMax) {
// extend the new partial alignment recursively
int64_t tmp_maxsc = hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
tempHit,
tempHit.rdoff(),
tempHit.len() + tempHit.trim3(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
maxsc = max<int64_t>(maxsc, tmp_maxsc);
} else {
local_genomeHits.push_back(tempHit);
}
}
}
}
// int64_t minsc = (rdi == 0 ? sink.bestUnp1() : sink.bestUnp2());
if(maxsc >= prev_score - sc.mmpMax) success = true;
if(!success &&
(him.localindexatts >= this->max_localindexatts || count == max_count || hierEbwtFw->prevLocalEbwt(localEbwtFw) == NULL)) {
for(index_t ti = 0; ti < local_genomeHits.size(); ti++) {
GenomeHit<index_t>& tempHit = local_genomeHits[ti];
int64_t minsc = this->_minsc[rdi];
if(!this->_secondary) {
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
}
if(tempHit.score() >= minsc) {
int64_t tmp_maxsc = hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
tempHit,
tempHit.rdoff(),
tempHit.len() + tempHit.trim3(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
maxsc = max<int64_t>(maxsc, tmp_maxsc);
}
}
}
} // while(!success && count++ < 2)
if(!success) {
if(hitoff > this->_minK &&
him.localindexatts < this->max_localindexatts) {
index_t extlen = 0;
index_t top = (index_t)OFF_MASK, bot = (index_t)OFF_MASK;
index_t extoff = hitoff - 1;
bool uniqueStop = true;
// perform global search for long introns
index_t nelt = this->globalEbwtSearch(
ebwtFw, // BWT index
rd, // read to align
sc, // scoring scheme
hit.fw(),
extoff,
extlen,
top,
bot,
rnd,
uniqueStop);
if(nelt <= 5 && extlen >= this->_minK) {
coords.clear();
bool straddled = false;
this->getGenomeCoords(
ebwtFw,
ref,
rnd,
top,
bot,
hit.fw(),
bot - top,
extoff + 1 - extlen,
extlen,
coords,
wlm,
prm,
him,
true, // reject straddled?
straddled);
assert_leq(coords.size(), nelt);
coords.sort();
for(int ri = coords.size() - 1; ri >= 0; ri--) {
const Coord& coord = coords[ri];
GenomeHit<index_t> tempHit;
tempHit.init(coord.orient(),
extoff + 1 - extlen,
extlen,
0, // trim5
0, // trim3
coord.ref(),
coord.off(),
this->_sharedVars);
if(!tempHit.compatibleWith(hit, this->_minIntronLen, this->_maxIntronLen, this->_no_spliced_alignment)) continue;
if(uniqueStop) {
assert_eq(coords.size(), 1);
index_t leftext = (index_t)OFF_MASK, rightext = (index_t)0;
tempHit.extend(rd, ref, ssdb, swa, swm, prm, sc, this->_minsc[rdi], rnd, this->_minK_local, this->_minIntronLen, this->_maxIntronLen, leftext, rightext);
}
int64_t minsc = this->_minsc[rdi];
bool combined = tempHit.combineWith(hit, rd, ref, ssdb, swa, swm, sc, minsc, rnd, this->_minK_local, this->_minIntronLen, this->_maxIntronLen);
if(!this->_secondary) {
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
}
if(combined && tempHit.score() >= minsc) {
assert_eq(tempHit.trim5(), 0);
assert_leq(tempHit.rdoff() + tempHit.len() + tempHit.trim3(), rdlen);
int64_t tmp_maxsc = hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
tempHit,
tempHit.rdoff(),
tempHit.len() + tempHit.trim3(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
maxsc = max<int64_t>(maxsc, tmp_maxsc);
}
}
}
}
GenomeHit<index_t> tempHit = hit;
// daehwan - for debugging purposes
if(tempHit.rdoff() <= 5 && false) {
index_t trim5 = tempHit.rdoff();
tempHit.trim5(trim5);
assert_leq(tempHit.len() + tempHit.trim5() + tempHit.trim3(), rdlen);
int64_t tmp_maxsc = hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
tempHit,
0,
tempHit.len() + tempHit.trim5() + tempHit.trim3(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
maxsc = max<int64_t>(maxsc, tmp_maxsc);
return maxsc;
}
// extend the partial alignment directly comparing with the corresponding genomic sequence
// with mismatches or a gap allowed
int64_t minsc = this->_minsc[rdi];
assert_geq(tempHit.score(), minsc);
index_t mm = (tempHit.score() - minsc) / sc.mmpMax;
index_t leftext = (index_t)OFF_MASK, rightext = (index_t)0;
index_t num_mismatch_allowed = 1;
if(hitoff <= this->_minK_local) {
num_mismatch_allowed = min<index_t>(tempHit.rdoff(), mm);
}
him.localextatts++;
tempHit.extend(rd, ref, ssdb, swa, swm, prm, sc, this->_minsc[rdi], rnd, this->_minK_local, this->_minIntronLen, this->_maxIntronLen, leftext, rightext, num_mismatch_allowed);
if(!this->_secondary) {
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
}
if(tempHit.score() >= minsc && leftext >= min<index_t>(this->_minK_local, hit.rdoff())) {
assert_eq(tempHit.trim5(), 0);
assert_leq(tempHit.rdoff() + tempHit.len() + tempHit.trim3(), rdlen);
int64_t tmp_maxsc = hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
tempHit,
tempHit.rdoff(),
tempHit.len() + tempHit.trim3(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
maxsc = max<int64_t>(maxsc, tmp_maxsc);
} else if(hitoff > this->_minK_local) {
// skip some bases of a read
index_t jumplen = hitoff > this->_minK ? this->_minK : this->_minK_local;
assert_leq(hitoff, hit.rdoff());
int64_t expected_score = hit.score() - (hit.rdoff() - hitoff) / jumplen * sc.mmpMax - sc.mmpMax;
if(expected_score >= minsc) {
assert_lt(hitlen + jumplen, rdlen);
assert_eq(hit.trim5(), 0);
assert_leq(hitoff + hitlen, rdlen);
int64_t tmp_maxsc = hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
hit,
hitoff - jumplen,
hitlen + jumplen,
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
maxsc = max<int64_t>(maxsc, tmp_maxsc);
}
}
}
} else {
// extend the partial alignment in the right direction
assert_lt(hitoff + hitlen, rdlen);
if(!ssdb.empty()) {
index_t fragoff = 0, fraglen = 0, right = 0;
hit.getRight(fragoff, fraglen, right);
const index_t minMatchLen = this->_minK_local;
// make use of a list of known or novel splice sites to further align the read
if(fraglen >= minMatchLen && !this->_no_spliced_alignment) {
spliceSites.clear();
assert_gt(fraglen, 0);
assert_leq(fragoff + fraglen, rdlen);
index_t right_unmapped_len = rdlen - fragoff - fraglen;
ssdb.getRightSpliceSites(hit.ref(), right + fraglen - minMatchLen, minMatchLen + min<index_t>(minMatchLen, right_unmapped_len), spliceSites);
for(size_t si = 0; si < spliceSites.size(); si++) {
const SpliceSite& ss = spliceSites[si];
if(!ss._fromfile && ss._readid + this->_thread_rids_mindist > rd.rdid) continue;
if(right > ss.left()) continue;
index_t frag2off = ss.right() - ss.left() + right + fraglen - 1;
GenomeHit<index_t> tempHit;
tempHit.init(hit.fw(),
fragoff + fraglen,
rdlen - fragoff - fraglen,
0, // trim5
0, // trim3
hit.ref(),
frag2off,
this->_sharedVars);
if(!hit.compatibleWith(tempHit, this->_minIntronLen, this->_maxIntronLen, this->_no_spliced_alignment)) continue;
GenomeHit<index_t> combinedHit = hit;
int64_t minsc = this->_minsc[rdi];
bool combined = combinedHit.combineWith(tempHit, rd, ref, ssdb, swa, swm, sc, minsc, rnd, this->_minK_local, this->_minIntronLen, this->_maxIntronLen, 1, 1, &ss);
if(!this->_secondary) {
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
}
index_t rightAnchorLen = 0, nedits = 0;
combinedHit.getRightAnchor(rightAnchorLen, nedits);
if(combined &&
combinedHit.score() >= minsc &&
nedits <= rightAnchorLen / 4) { // prevent (short) anchors from having many mismatches
assert_leq(combinedHit.trim5(), combinedHit.rdoff());
assert_eq(combinedHit.rdoff() + combinedHit.len(), rdlen);
int64_t tmp_maxsc = hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
combinedHit,
combinedHit.rdoff() - combinedHit.trim5(),
combinedHit.len() + combinedHit.trim5(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
maxsc = max<int64_t>(maxsc, tmp_maxsc);
}
}
}
}
bool use_localindex = true;
if(hit.len() == hitlen && hitoff + hitlen + this->_minK > rdlen) {
index_t leftext = (index_t)0, rightext = (index_t)OFF_MASK;
GenomeHit<index_t> tempHit = hit;
tempHit.extend(rd, ref, ssdb, swa, swm, prm, sc, this->_minsc[rdi], rnd, this->_minK_local, this->_minIntronLen, this->_maxIntronLen, leftext, rightext, 1);
if(tempHit.rdoff() + tempHit.len()== rdlen) {
use_localindex = false;
}
}
// choose a local index based on the genomic location of the partial alignment
const HierEbwt<index_t, local_index_t>* hierEbwtFw = (const HierEbwt<index_t, local_index_t>*)(&ebwtFw);
const LocalEbwt<local_index_t, index_t>* localEbwtFw = hierEbwtFw->getLocalEbwt(hit.ref(), hit.refoff());
bool success = false, first = true;
index_t count = 0;
index_t max_count = 2;
int64_t prev_score = hit.score();
local_genomeHits.clear();
while(!success && count++ < max_count && use_localindex) {
if(him.localindexatts >= this->max_localindexatts) break;
if(first) {
first = false;
} else {
localEbwtFw = hierEbwtFw->nextLocalEbwt(localEbwtFw);
if(localEbwtFw == NULL || localEbwtFw->empty()) break;
}
// local index search
index_t extlen = 0;
local_index_t top = (local_index_t)OFF_MASK, bot = (local_index_t)OFF_MASK;
index_t extoff = hitoff + hitlen + this->_minK_local;
if(extoff + 1 < rdlen) extoff += 1;
if(extoff >= rdlen) {
extoff = rdlen - 1;
}
index_t nelt = (index_t)OFF_MASK;
index_t max_nelt = std::max<index_t>(5, extlen);
bool no_extension = false;
bool uniqueStop;
index_t minUniqueLen = this->_minK_local;
index_t maxHitLen = max<index_t>(extoff - hitoff - hitlen, this->_minK_local);
for(; maxHitLen < extoff + 1 && extoff < rdlen;) {
extlen = 0;
uniqueStop = false;
him.localindexatts++;
nelt = this->localEbwtSearch(
localEbwtFw, // BWT index
NULL, // BWT index
rd, // read to align
sc, // scoring scheme
hit.fw(),
false, // searchfw,
extoff,
extlen,
top,
bot,
rnd,
uniqueStop,
minUniqueLen,
maxHitLen);
if(extoff < hitoff + hitlen) {
no_extension = true;
break;
}
if(nelt <= max_nelt) break;
if(extoff + 1 < rdlen) extoff++;
else {
if(extlen < maxHitLen) break;
else maxHitLen++;
}
}
assert_leq(top, bot);
assert_eq(nelt, (index_t)(bot - top));
assert_leq(extlen, extoff + 1);
assert_leq(extoff, rdlen);
if(nelt > 0 &&
nelt <= max_nelt &&
extlen >= minAnchorLen &&
!no_extension) {
assert_leq(nelt, max_nelt);
coords.clear();
bool straddled = false;
// get genomic locations for this local search
this->getGenomeCoords_local(
*localEbwtFw,
ref,
rnd,
top,
bot,
hit.fw(),
extoff + 1 - extlen,
extlen,
coords,
wlm,
prm,